1
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Li T, Ferraro N, Strober BJ, Aguet F, Kasela S, Arvanitis M, Ni B, Wiel L, Hershberg E, Ardlie K, Arking DE, Beer RL, Brody J, Blackwell TW, Clish C, Gabriel S, Gerszten R, Guo X, Gupta N, Johnson WC, Lappalainen T, Lin HJ, Liu Y, Nickerson DA, Papanicolaou G, Pritchard JK, Qasba P, Shojaie A, Smith J, Sotoodehnia N, Taylor KD, Tracy RP, Van Den Berg D, Wheeler MT, Rich SS, Rotter JI, Battle A, Montgomery SB. The functional impact of rare variation across the regulatory cascade. Cell Genom 2023; 3:100401. [PMID: 37868038 PMCID: PMC10589633 DOI: 10.1016/j.xgen.2023.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/08/2023] [Accepted: 08/10/2023] [Indexed: 10/24/2023]
Abstract
Each human genome has tens of thousands of rare genetic variants; however, identifying impactful rare variants remains a major challenge. We demonstrate how use of personal multi-omics can enable identification of impactful rare variants by using the Multi-Ethnic Study of Atherosclerosis, which included several hundred individuals, with whole-genome sequencing, transcriptomes, methylomes, and proteomes collected across two time points, 10 years apart. We evaluated each multi-omics phenotype's ability to separately and jointly inform functional rare variation. By combining expression and protein data, we observed rare stop variants 62 times and rare frameshift variants 216 times as frequently as controls, compared to 13-27 times as frequently for expression or protein effects alone. We extended a Bayesian hierarchical model, "Watershed," to prioritize specific rare variants underlying multi-omics signals across the regulatory cascade. With this approach, we identified rare variants that exhibited large effect sizes on multiple complex traits including height, schizophrenia, and Alzheimer's disease.
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Affiliation(s)
- Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole Ferraro
- Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA
| | - Benjamin J. Strober
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Harvard School of Public Health, Epidemiology Department, Boston, MA, USA
| | | | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Marios Arvanitis
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Division of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Bohan Ni
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Laurens Wiel
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca L. Beer
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Robert Gerszten
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - W. Craig Johnson
- Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Henry J. Lin
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - George Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Pankaj Qasba
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington School of Public Health, Seattle, WA, USA
| | - Josh Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell P. Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - David Van Den Berg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matthew T. Wheeler
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Malone Center for Engineering of Healthcare, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
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2
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Pinard A, Ye W, Fraser SM, Rosenfeld JA, Pichurin P, Hickey SE, Guo D, Cecchi AC, Boerio ML, Guey S, Aloui C, Lee K, Kraemer M, Alyemni SO, Bamshad MJ, Nickerson DA, Tournier-Lasserve E, Haider S, Jin SC, Smith ER, Kahle KT, Jan LY, He M, Milewicz DM. Rare variants in ANO1, encoding a calcium-activated chloride channel, predispose to moyamoya disease. Brain 2023; 146:3616-3623. [PMID: 37253099 PMCID: PMC10473557 DOI: 10.1093/brain/awad172] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/24/2023] [Accepted: 04/16/2023] [Indexed: 06/01/2023] Open
Abstract
Moyamoya disease, a cerebrovascular disease leading to strokes in children and young adults, is characterized by progressive occlusion of the distal internal carotid arteries and the formation of collateral vessels. Altered genes play a prominent role in the aetiology of moyamoya disease, but a causative gene is not identified in the majority of cases. Exome sequencing data from 151 individuals from 84 unsolved families were analysed to identify further genes for moyamoya disease, then candidate genes assessed in additional cases (150 probands). Two families had the same rare variant in ANO1, which encodes a calcium-activated chloride channel, anoctamin-1. Haplotype analyses found the families were related, and ANO1 p.Met658Val segregated with moyamoya disease in the family with an LOD score of 3.3. Six additional ANO1 rare variants were identified in moyamoya disease families. The ANO1 rare variants were assessed using patch-clamp recordings, and the majority of variants, including ANO1 p.Met658Val, displayed increased sensitivity to intracellular Ca2+. Patients harbouring these gain-of-function ANO1 variants had classic features of moyamoya disease, but also had aneurysm, stenosis and/or occlusion in the posterior circulation. Our studies support that ANO1 gain-of-function pathogenic variants predispose to moyamoya disease and are associated with unique involvement of the posterior circulation.
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Affiliation(s)
- Amélie Pinard
- Department of Internal Medicine, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wenlei Ye
- Howard Hughes Medical Institute, Department of Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Stuart M Fraser
- Department of Pediatrics, Division of Child Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pavel Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55902, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
- Division of Genetic and Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Dongchuan Guo
- Department of Internal Medicine, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Alana C Cecchi
- Department of Internal Medicine, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Maura L Boerio
- Department of Internal Medicine, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Stéphanie Guey
- Université de Paris, Inserm U1141, AP-HP Groupe hospitalier Lariboisière Saint Louis, 75019 Paris, France
| | - Chaker Aloui
- Université de Paris, Inserm U1141, AP-HP Groupe hospitalier Lariboisière Saint Louis, 75019 Paris, France
| | - Kwanghyuk Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Markus Kraemer
- Department of Neurology, Alfried Krupp-Hospital, 45131 Essen, Germany
- Department of Neurology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | | | | | - Michael J Bamshad
- Division of Genetics Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Elisabeth Tournier-Lasserve
- Université de Paris, Inserm U1141, AP-HP Groupe hospitalier Lariboisière Saint Louis, 75019 Paris, France
- AP-HP, Service de génétique moléculaire neurovasculaire, Centre de Référence des Maladies Vasculaires Rares du Cerveau et de l’oeil, Groupe Hospitalier Saint-Louis Lariboisière, 75010 Paris, France
| | - Shozeb Haider
- UCL School of Pharmacy, Bloomsbury, London WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, UK
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Edward R Smith
- Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Lily Yeh Jan
- Howard Hughes Medical Institute, Department of Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mu He
- Howard Hughes Medical Institute, Department of Physiology, University of California San Francisco, San Francisco, CA 94158, USA
- School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Dianna M Milewicz
- Department of Internal Medicine, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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3
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Liu Q, Zhou Y, Cogan JD, Mitchell DB, Sheng Q, Zhao S, Bai Y, Ciombor KK, Sabusap CM, Malabanan MM, Markin CR, Douglas K, Ding G, Banovich NE, Nickerson DA, Blue EE, Bamshad MJ, Brown KK, Schwartz DA, Phillips JA, Martinez-Barricarte R, Salisbury ML, Shyr Y, Loyd JE, Kropski JA, Blackwell TS. The Genetic Landscape of Familial Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 207:1345-1357. [PMID: 36622818 PMCID: PMC10595451 DOI: 10.1164/rccm.202204-0781oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 01/09/2023] [Indexed: 01/10/2023] Open
Abstract
Rationale and Objectives: Up to 20% of idiopathic interstitial lung disease is familial, referred to as familial pulmonary fibrosis (FPF). An integrated analysis of FPF genetic risk was performed by comprehensively evaluating for genetic rare variants (RVs) in a large cohort of FPF kindreds. Methods: Whole-exome sequencing and/or candidate gene sequencing from affected individuals in 569 FPF kindreds was performed, followed by cosegregation analysis in large kindreds, gene burden analysis, gene-based risk scoring, cell-type enrichment analysis, and coexpression network construction. Measurements and Main Results: It was found that 14.9-23.4% of genetic risk in kindreds could be explained by RVs in genes previously linked to FPF, predominantly telomere-related genes. New candidate genes were identified in a small number of families-including SYDE1, SERPINB8, GPR87, and NETO1-and tools were developed for evaluation and prioritization of RV-containing genes across kindreds. Several pathways were enriched for RV-containing genes in FPF, including focal adhesion and mitochondrial complex I assembly. By combining single-cell transcriptomics with prioritized candidate genes, expression of RV-containing genes was discovered to be enriched in smooth muscle cells, type II alveolar epithelial cells, and endothelial cells. Conclusions: In the most comprehensive FPF genetic study to date, the prevalence of RVs in known FPF-related genes was defined, and new candidate genes and pathways relevant to FPF were identified. However, new RV-containing genes shared across multiple kindreds were not identified, thereby suggesting that heterogeneous genetic variants involving a variety of genes and pathways mediate genetic risk in most FPF kindreds.
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Affiliation(s)
- Qi Liu
- Department of Biostatistics
| | | | - Joy D. Cogan
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics
| | | | | | | | | | | | | | | | | | | | - Guixiao Ding
- Division of Allergy, Pulmonary and Critical Care Medicine
| | | | | | | | - Michael J. Bamshad
- Department of Genome Sciences
- Brotman-Baty Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - David A. Schwartz
- Department of Medicine, School of Medicine, University of Colorado Denver, Denver, Colorado; and
| | - John A. Phillips
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics
| | | | | | | | - James E. Loyd
- Division of Allergy, Pulmonary and Critical Care Medicine
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Timothy S. Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
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4
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Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. Res Sq 2023:rs.3.rs-2515453. [PMID: 36778386 PMCID: PMC9915771 DOI: 10.21203/rs.3.rs-2515453/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
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Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
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5
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Esterhuizen AI, Tiffin N, Riordan G, Wessels M, Burman RJ, Aziz MC, Calhoun JD, Gunti J, Amiri EE, Ramamurthy A, Bamshad MJ, Mefford HC, Ramesar R, Wilmshurst JM, Carvill GL, Leal SM, Nickerson DA, Anderson P, Bacus TJ, Blue EE, Brower K, Buckingham KJ, Chong JX, Cornejo Sánchez D, Davis CP, Davis CJ, Frazar CD, Gomeztagle-Burgess K, Gordon WW, Horike-Pyne M, Hurless JR, Jarvik GP, Johanson E, Thomas Kolar J, Marvin CT, McGee S, McGoldrick DJ, Mekonnen B, Nielsen PM, Patterson K, Radhakrishnan A, Richardson MA, Roote GT, Ryke EL, Schrauwen I, Shively KM, Smith JD, Tackett M, Wang G, Weiss JM, Wheeler MM, Yi Q, Zhang X. Precision medicine for developmental and epileptic encephalopathies in Africa-strategies for a resource-limited setting. Genet Med 2023; 25:100333. [PMID: 36480001 DOI: 10.1016/j.gim.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Sub-Saharan Africa bears the highest burden of epilepsy worldwide. A presumed proportion is genetic, but this etiology is buried under the burden of infections and perinatal insults in a setting of limited awareness and few options for testing. Children with developmental and epileptic encephalopathies (DEEs) are most severely affected by this diagnostic gap in Africa, because the rate of actionable findings is highest in DEE-associated genes. METHODS We tested 234 genetically naive South African children diagnosed with/possible DEE using gene panels, exome sequencing, and chromosomal microarray. Statistical comparison of electroclinical features in children with and children without candidate variants was performed to identify characteristics most likely predictive of a positive genetic finding. RESULTS Of the 41 (of 234) children with likely/pathogenic variants, 26 had variants supporting precision therapy. Multivariate regression modeling highlighted neonatal or infantile-onset seizures and movement abnormalities as predictive of a positive genetic finding. We used this, coupled with an emphasis on precision medicine outcomes, to propose the pragmatic "Think-Genetics" strategy for early recognition of a possible genetic etiology. CONCLUSION Our findings emphasize the importance of an early genetic diagnosis in DEE. We designed the Think-Genetics strategy for early recognition, appropriate interim management, and genetic testing for DEE in resource-constrained settings.
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Affiliation(s)
- Alina I Esterhuizen
- The South African MRC/UCT Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Nicki Tiffin
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Gillian Riordan
- Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Marie Wessels
- Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Richard J Burman
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Miriam C Aziz
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jeffrey D Calhoun
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jonathan Gunti
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Ezra E Amiri
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Aishwarya Ramamurthy
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA; Department of Genome Sciences, University of Washington, Seattle, WA; Brotman Baty Institute, Seattle, WA
| | | | - Heather C Mefford
- Centre for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN
| | - Raj Ramesar
- The South African MRC/UCT Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Jo M Wilmshurst
- Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, Neuroscience Institute, University of Cape Town, Cape Town, South Africa.
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL; Department of Pharmacology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL.
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6
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Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. bioRxiv 2023:2023.01.25.525428. [PMID: 36747810 PMCID: PMC9900832 DOI: 10.1101/2023.01.25.525428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
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Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
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7
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Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, Þorsteinsdóttir U, Magnússon MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun 2022; 13:7592. [PMID: 36481753 PMCID: PMC9732337 DOI: 10.1038/s41467-022-35354-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.
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Affiliation(s)
- Marsha M. Wheeler
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98105 USA
| | - Adrienne M. Stilp
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Shuquan Rao
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA ,grid.506261.60000 0001 0706 7839State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020 China
| | - Bjarni V. Halldórsson
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.9580.40000 0004 0643 5232School of Technology, Reykjavik University, Reykjavík, Iceland
| | - Doruk Beyter
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Jia Wen
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Anna V. Mihkaylova
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Caitlin P. McHugh
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - John Lane
- grid.17635.360000000419368657Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Min-Zhi Jiang
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Laura M. Raffield
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Goo Jun
- grid.267308.80000 0000 9206 2401Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Fritz J. Sedlazeck
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Ginger Metcalf
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Yao Yao
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Joshua B. Bis
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Nathalie Chami
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Paul S. de Vries
- grid.267308.80000 0000 9206 2401Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Pinkal Desai
- grid.5386.8000000041936877XDivision of Hematology and Oncology, Weill Cornell Medical College, New York, NY 10065 USA
| | - James S. Floyd
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Yan Gao
- grid.251313.70000 0001 2169 2489Jackson Heart Study, Department of Medicine, University of Mississippi, Jackson, MS 39216 USA
| | - Kai Kammers
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Wonji Kim
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 2115 USA
| | - Jee-Young Moon
- grid.251993.50000000121791997Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Aakrosh Ratan
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
| | - Lisa R. Yanek
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Laura Almasy
- grid.25879.310000 0004 1936 8972Children’s Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
| | - Lewis C. Becker
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - John Blangero
- grid.449717.80000 0004 5374 269XDepartment of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520 USA
| | - Michael H. Cho
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 2115 USA
| | - Joanne E. Curran
- grid.449717.80000 0004 5374 269XDepartment of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520 USA
| | - Myriam Fornage
- grid.267308.80000 0000 9206 2401Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Robert C. Kaplan
- grid.251993.50000000121791997Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Joshua P. Lewis
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD USA
| | - Ruth J. F. Loos
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Braxton D. Mitchell
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD USA
| | - Alanna C. Morrison
- grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Michael Preuss
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Bruce M. Psaty
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Stephen S. Rich
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
| | - Jerome I. Rotter
- grid.513199.6The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Hua Tang
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Russell P. Tracy
- grid.59062.380000 0004 1936 7689Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT 5446 USA
| | - Eric Boerwinkle
- grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Goncalo R. Abecasis
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Thomas W. Blackwell
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Albert V. Smith
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Andrew D. Johnson
- grid.279885.90000 0001 2293 4638Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 1702 USA
| | - Rasika A. Mathias
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Deborah A. Nickerson
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98105 USA
| | - Matthew P. Conomos
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Yun Li
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Unnur Þorsteinsdóttir
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Magnús K. Magnússon
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Kari Stefansson
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Nathan D. Pankratz
- grid.17635.360000000419368657Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Daniel E. Bauer
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Paul L. Auer
- grid.30760.320000 0001 2111 8460Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Alex P. Reiner
- grid.34477.330000000122986657Department of Epidemiology, University of Washington, Seattle, WA 98105 USA
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8
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Chung E, Magedson A, Emanuels A, Luiten K, Pfau B, Truong M, Chow EJ, Hughes JP, Uyeki TM, Englund JA, Nickerson DA, Lockwood CM, Shendure J, Starita LM, Chu HY. SARS-CoV-2 Screening Testing in Schools: A Comparison of School- Vs. Home-Based Collection Methods. J Pediatric Infect Dis Soc 2022; 11:522-524. [PMID: 36082698 PMCID: PMC9494399 DOI: 10.1093/jpids/piac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We implemented a voluntary SARS-CoV-2 screening testing study for kindergarten-2nd grade students in a Washington School district. Weekly SARS-CoV-2 testing participation was higher for students with staff-collected nasal swabs at school than for students with parent-collected swabs at home.
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Affiliation(s)
- Erin Chung
- Corresponding Author: Erin Chung, MD, Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, UW Medicine Box 358061, Chu Lab Room E691,750 Republican Street, Seattle, WA 98109, USA. E-mal:
| | | | - Anne Emanuels
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kyle Luiten
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA
| | - Melissa Truong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Eric J Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, Washington, USA,Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Christina M Lockwood
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
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9
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Patel RA, Musharoff SA, Spence JP, Pimentel H, Tcheandjieu C, Mostafavi H, Sinnott-Armstrong N, Clarke SL, Smith CJ, Durda PP, Taylor KD, Tracy R, Liu Y, Johnson WC, Aguet F, Ardlie KG, Gabriel S, Smith J, Nickerson DA, Rich SS, Rotter JI, Tsao PS, Assimes TL, Pritchard JK. Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits. Am J Hum Genet 2022; 109:1286-1297. [PMID: 35716666 PMCID: PMC9300878 DOI: 10.1016/j.ajhg.2022.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/26/2022] [Indexed: 01/09/2023] Open
Abstract
Despite the growing number of genome-wide association studies (GWASs), it remains unclear to what extent gene-by-gene and gene-by-environment interactions influence complex traits in humans. The magnitude of genetic interactions in complex traits has been difficult to quantify because GWASs are generally underpowered to detect individual interactions of small effect. Here, we develop a method to test for genetic interactions that aggregates information across all trait-associated loci. Specifically, we test whether SNPs in regions of European ancestry shared between European American and admixed African American individuals have the same causal effect sizes. We hypothesize that in African Americans, the presence of genetic interactions will drive the causal effect sizes of SNPs in regions of European ancestry to be more similar to those of SNPs in regions of African ancestry. We apply our method to two traits: gene expression in 296 African Americans and 482 European Americans in the Multi-Ethnic Study of Atherosclerosis (MESA) and low-density lipoprotein cholesterol (LDL-C) in 74K African Americans and 296K European Americans in the Million Veteran Program (MVP). We find significant evidence for genetic interactions in our analysis of gene expression; for LDL-C, we observe a similar point estimate, although this is not significant, most likely due to lower statistical power. These results suggest that gene-by-gene or gene-by-environment interactions modify the effect sizes of causal variants in human complex traits.
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Affiliation(s)
- Roshni A Patel
- Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Shaila A Musharoff
- Genetics, Stanford University School of Medicine, Stanford, CA, USA; VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Jeffrey P Spence
- Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Harold Pimentel
- Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Catherine Tcheandjieu
- VA Palo Alto Health Care System, Palo Alto, CA, USA; Stanford University School of Medicine, Stanford, CA, USA
| | | | - Nasa Sinnott-Armstrong
- Genetics, Stanford University School of Medicine, Stanford, CA, USA; VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Shoa L Clarke
- VA Palo Alto Health Care System, Palo Alto, CA, USA; Stanford University School of Medicine, Stanford, CA, USA
| | - Courtney J Smith
- Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter P Durda
- The Robert Larner, M.D. College of Medicine at The University of Vermont, Burlington, VT, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell Tracy
- The Robert Larner, M.D. College of Medicine at The University of Vermont, Burlington, VT, USA
| | - Yongmei Liu
- Duke University School of Medicine, Durham, NC, USA
| | | | | | | | | | - Josh Smith
- Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, CA, USA; Stanford University School of Medicine, Stanford, CA, USA
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, USA; Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan K Pritchard
- Genetics, Stanford University School of Medicine, Stanford, CA, USA; Biology, Stanford University, Stanford, CA, USA.
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10
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Shimada S, Ng BG, White AL, Nickander KK, Turgeon C, Liedtke KL, Lam CT, Font-Montgomery E, Lourenço CM, He M, Peck DS, Umaña LA, Uhles CL, Haynes D, Wheeler PG, Bamshad MJ, Nickerson DA, Cushing T, Gates R, Gomez-Ospina N, Byers HM, Scalco FB, Martinez NN, Sachdev R, Smith L, Poduri A, Malone S, Harris R, Scheffer IE, Rosenzweig SD, Adams DR, Gahl WA, Malicdan MCV, Raymond KM, Freeze HH, Wolfe LA. Clinical, biochemical and genetic characteristics of MOGS-CDG: a rare congenital disorder of glycosylation. J Med Genet 2022; 59:jmedgenet-2021-108177. [PMID: 35790351 PMCID: PMC9813274 DOI: 10.1136/jmedgenet-2021-108177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/18/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE To summarise the clinical, molecular and biochemical phenotype of mannosyl-oligosaccharide glucosidase-related congenital disorders of glycosylation (MOGS-CDG), which presents with variable clinical manifestations, and to analyse which clinical biochemical assay consistently supports diagnosis in individuals with bi-allelic variants in MOGS. METHODS Phenotypic characterisation was performed through an international and multicentre collaboration. Genetic testing was done by exome sequencing and targeted arrays. Biochemical assays on serum and urine were performed to delineate the biochemical signature of MOGS-CDG. RESULTS Clinical phenotyping revealed heterogeneity in MOGS-CDG, including neurological, immunological and skeletal phenotypes. Bi-allelic variants in MOGS were identified in 12 individuals from 11 families. The severity in each organ system was variable, without definite genotype correlation. Urine oligosaccharide analysis was consistently abnormal for all affected probands, whereas other biochemical analyses such as serum transferrin analysis was not consistently abnormal. CONCLUSION The clinical phenotype of MOGS-CDG includes multisystemic involvement with variable severity. Molecular analysis, combined with biochemical testing, is important for diagnosis. In MOGS-CDG, urine oligosaccharide analysis via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry can be used as a reliable biochemical test for screening and confirmation of disease.
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Affiliation(s)
- Shino Shimada
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Amy L. White
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kim. K. Nickander
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Coleman Turgeon
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kristen L. Liedtke
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Christina T. Lam
- Division of Genetic Medicine, Department of Pediatrics, Seattle Children’s Hospital and University of Washington, Seattle, WA, USA
| | | | - Charles M. Lourenço
- Faculdade de Medicina, Centro Universitario Estácio de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Neurogenetics Unit, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
| | - Miao He
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dawn S. Peck
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Luis A. Umaña
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Crescenda L. Uhles
- Department of Genetics, Children’s Medical Center Dallas, Dallas, TX, USA
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, USA
| | - Patricia G. Wheeler
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, USA
| | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Tom Cushing
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Ryan Gates
- Division of Medical Genetics, Stanford University, Stanford, CA, USA
| | | | - Heather M. Byers
- Division of Medical Genetics, Stanford University, Stanford, CA, USA
| | | | - Fernanda B. Scalco
- Laboratório de Erros Inatos do Metabolismo/LABEIM, Instituto de Química, Universidade Federal do Rio de Janeiro, Departamento de Bioquímica, Avenida Horácio Macedo, 1281, Bloco C, Polo de Química, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Noelia N. Martinez
- Center for Clinical Genetics, Sydney Children’s Hospital-Randwick, Sydney, New South Wales, Australia
| | - Rani Sachdev
- Center for Clinical Genetics, Sydney Children’s Hospital-Randwick, Sydney, New South Wales, Australia
- School of Women’s & Children’s Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Lacey Smith
- Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Annapurna Poduri
- Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen Malone
- Department of Neurosciences, Queensland Children’s Hospital, Brisbane, Queensland, Australia
| | - Rebekah Harris
- Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Ingrid E. Scheffer
- Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Department of Pediatrics, The University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
- Murdoch Children’s Research Institute and Florey Institute, Melbourne, VIC, Australia
| | - Sergio D. Rosenzweig
- Department of Laboratory Medicine, Clinical Center, and Primary Immunodeficiency Clinic, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - David R. Adams
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William A. Gahl
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - May CV. Malicdan
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Senior authors and contributed equally
| | - Kimiyo M. Raymond
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Senior authors and contributed equally
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, CA, USA
- Senior authors and contributed equally
| | - Lynne A. Wolfe
- Medical Genetic Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Senior authors and contributed equally
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11
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Li J, Yang W, Wang YJ, Ma C, Curry CJ, McGoldrick D, Nickerson DA, Chong JX, Blue EE, Mullikin JC, Reefhuis J, Nembhard WN, Romitti PA, Werler MM, Browne ML, Olshan AF, Finnell RH, Feldkamp ML, Pangilinan F, Almli LM, Bamshad MJ, Brody LC, Jenkins MM, Shaw GM. Exome sequencing identifies genetic variants in anophthalmia and microphthalmia. Am J Med Genet A 2022; 188:2376-2388. [PMID: 35716026 PMCID: PMC9283271 DOI: 10.1002/ajmg.a.62874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/10/2022]
Abstract
Anophthalmia and microphthalmia (A/M) are rare birth defects affecting up to 2 per 10,000 live births. These conditions are manifested by the absence of an eye or reduced eye volumes within the orbit leading to vision loss. Although clinical case series suggest a strong genetic component in A/M, few systematic investigations have been conducted on potential genetic contributions owing to low population prevalence. To overcome this challenge, we utilized DNA samples and data collected as part of the National Birth Defects Prevention Study (NBDPS). The NBDPS employed multi-center ascertainment of infants affected by A/M. We performed exome sequencing on 67 family trios and identified numerous genes affected by rare deleterious nonsense and missense variants in this cohort, including de novo variants. We identified 9 nonsense changes and 86 missense variants that are absent from the reference human population (Genome Aggregation Database), and we suggest that these are high priority candidate genes for A/M. We also performed literature curation, single cell transcriptome comparisons, and molecular pathway analysis on the candidate genes and performed protein structure modeling to determine the potential pathogenic variant consequences on PAX6 in this disease.
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Affiliation(s)
- Jingjing Li
- Department of Neurology School of Medicine, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, The Bakar Computational Health Sciences Institute, The Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, California, USA
| | - Wei Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Yuejun Jessie Wang
- Department of Neurology School of Medicine, The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, The Bakar Computational Health Sciences Institute, The Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, California, USA
| | - Chen Ma
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Cynthia J Curry
- Genetic Medicine, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Daniel McGoldrick
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Elizabeth E Blue
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James C Mullikin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennita Reefhuis
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wendy N Nembhard
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Paul A Romitti
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, Iowa, USA
| | - Martha M Werler
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Marilyn L Browne
- Birth Defects Registry, New York State Department of Health, Albany, New York, USA.,Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, New York, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Richard H Finnell
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA.,Department of Molecular and Human Genetics, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA.,Department of Medicine, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Marcia L Feldkamp
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Faith Pangilinan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lynn M Almli
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mike J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Lawrence C Brody
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | -
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland, USA
| | -
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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12
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Gaik M, Kojic M, Stegeman MR, Öncü-Öner T, Kościelniak A, Jones A, Mohamed A, Chau PYS, Sharmin S, Chramiec-Głąbik A, Indyka P, Rawski M, Biela A, Dobosz D, Millar A, Chau V, Ünalp A, Piper M, Bellingham MC, Eichler EE, Nickerson DA, Güleryüz H, Abbassi NEH, Jazgar K, Davis MJ, Mercimek-Andrews S, Cingöz S, Wainwright BJ, Glatt S. Functional divergence of the two Elongator subcomplexes during neurodevelopment. EMBO Mol Med 2022; 14:e15608. [PMID: 35698786 PMCID: PMC9260213 DOI: 10.15252/emmm.202115608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022] Open
Abstract
The highly conserved Elongator complex is a translational regulator that plays a critical role in neurodevelopment, neurological diseases, and brain tumors. Numerous clinically relevant variants have been reported in the catalytic Elp123 subcomplex, while no missense mutations in the accessory subcomplex Elp456 have been described. Here, we identify ELP4 and ELP6 variants in patients with developmental delay, epilepsy, intellectual disability, and motor dysfunction. We determine the structures of human and murine Elp456 subcomplexes and locate the mutated residues. We show that patient‐derived mutations in Elp456 affect the tRNA modification activity of Elongator in vitro as well as in human and murine cells. Modeling the pathogenic variants in mice recapitulates the clinical features of the patients and reveals neuropathology that differs from the one caused by previously characterized Elp123 mutations. Our study demonstrates a direct correlation between Elp4 and Elp6 mutations, reduced Elongator activity, and neurological defects. Foremost, our data indicate previously unrecognized differences of the Elp123 and Elp456 subcomplexes for individual tRNA species, in different cell types and in different key steps during the neurodevelopment of higher organisms.
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Affiliation(s)
- Monika Gaik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marija Kojic
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Megan R Stegeman
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Tülay Öncü-Öner
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ahmed Mohamed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Colonial Foundation Healthy Ageing Centre, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,The Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Pak Yan Stefanie Chau
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Sazia Sharmin
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Paulina Indyka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dominika Dobosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Amanda Millar
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Vann Chau
- Department of Paediatrics (Neurology), The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Aycan Ünalp
- Department of Pediatric Neurology, Dr. Behçet Uz Children's Hospital, İzmir, Turkey
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Mark C Bellingham
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Handan Güleryüz
- Department of Pediatric Radiology, School of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Nour El Hana Abbassi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Konrad Jazgar
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Melissa J Davis
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,The Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia.,The Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Saadet Mercimek-Andrews
- The Hospital for Sick Children, Toronto, ON, Canada.,Department of Medical Genetics, Faculty of Medicine and Dentistry, The University of Alberta, Edmonton, AB, Canada
| | - Sultan Cingöz
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Brandon J Wainwright
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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13
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Cingöz S, Soydemir D, Öner TÖ, Karaca E, Özden B, Kurul SH, Bayram E, Coe BP, Nickerson DA, Eichler EE. Novel biallelic variants affecting the OTU domain of the gene OTUD6B associate with severe intellectual disability syndrome and molecular dynamics simulations. Eur J Med Genet 2022; 65:104497. [PMID: 35430327 PMCID: PMC9448893 DOI: 10.1016/j.ejmg.2022.104497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/13/2022] [Accepted: 03/29/2022] [Indexed: 01/25/2023]
Abstract
Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies (IDDFSDA) is an autosomal recessive multisystem disorder caused by compound heterozygous or homozygous variants in the gene OTUD6B. Herein, we describe novel pathogenic compound heterozygous variants in OTUD6B identified via whole-exome sequencing in an index case exhibited the severe IDDFSDA phenotype. The potential pathogenicity of the novel frameshift and missense variants in the index case was investigated using in silico tools. The truncating frameshift variant in one allele was predicted to undergo degradation via nonsense-mediated decay of the mRNA molecule. To predict the severity of the damage to the protein caused by the missense variant in the other allele and its effects on phenotypic severity was further investigated together with a previously reported first homozygous missense variant in the same domain in another patient with a less severe IDDFSDA phenotype using structural modeling and molecular dynamics (MD) simulations for the first time. Based on these analyzes, it is anticipated that Tyr216Cys in the earlier reported case with less severe IDDFSDA will lead to localized destabilization, whereas Ile274Arg in the presented index case with the severe IDDFSDA phenotype will lead to significant distortion in the overall fold of OTUD6B. Our findings suggest that compound LOF and ultrarare missense variants may be contribute to the underlying variability expressivity associated with this disorder. In conclusion, our findings support that the clinical severity could be related with the predicted functional severity of the variations in OTUD6B. However, additional functional studies are required.
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Affiliation(s)
- Sultan Cingöz
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
| | - Didem Soydemir
- Department of Pediatrics, Division of Child Neurology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Tülay Öncü Öner
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul Health Campus, Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Burcu Özden
- Izmir Biomedicine and Genome Center, Dokuz Eylul Health Campus, Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Semra Hız Kurul
- Department of Pediatrics, Division of Child Neurology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylul Health Campus, Izmir, Turkey
| | - Erhan Bayram
- Department of Pediatrics, Division of Child Neurology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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14
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Hu X, Qiao D, Kim W, Moll M, Balte PP, Lange LA, Bartz TM, Kumar R, Li X, Yu B, Cade BE, Laurie CA, Sofer T, Ruczinski I, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Gabriel S, Gupta N, Dugan-Perez S, Cupples LA, Loehr LR, Jain D, Rotter JI, Wilson JG, Psaty BM, Fornage M, Morrison AC, Vasan RS, Washko G, Rich SS, O'Connor GT, Bleecker E, Kaplan RC, Kalhan R, Redline S, Gharib SA, Meyers D, Ortega V, Dupuis J, London SJ, Lappalainen T, Oelsner EC, Silverman EK, Barr RG, Thornton TA, Wheeler HE, Cho MH, Im HK, Manichaikul A. Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program. Am J Hum Genet 2022; 109:857-870. [PMID: 35385699 PMCID: PMC9118106 DOI: 10.1016/j.ajhg.2022.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/04/2022] [Indexed: 12/17/2022] Open
Abstract
While polygenic risk scores (PRSs) enable early identification of genetic risk for chronic obstructive pulmonary disease (COPD), predictive performance is limited when the discovery and target populations are not well matched. Hypothesizing that the biological mechanisms of disease are shared across ancestry groups, we introduce a PrediXcan-derived polygenic transcriptome risk score (PTRS) to improve cross-ethnic portability of risk prediction. We constructed the PTRS using summary statistics from application of PrediXcan on large-scale GWASs of lung function (forced expiratory volume in 1 s [FEV1] and its ratio to forced vital capacity [FEV1/FVC]) in the UK Biobank. We examined prediction performance and cross-ethnic portability of PTRS through smoking-stratified analyses both on 29,381 multi-ethnic participants from TOPMed population/family-based cohorts and on 11,771 multi-ethnic participants from TOPMed COPD-enriched studies. Analyses were carried out for two dichotomous COPD traits (moderate-to-severe and severe COPD) and two quantitative lung function traits (FEV1 and FEV1/FVC). While the proposed PTRS showed weaker associations with disease than PRS for European ancestry, the PTRS showed stronger association with COPD than PRS for African Americans (e.g., odds ratio [OR] = 1.24 [95% confidence interval [CI]: 1.08-1.43] for PTRS versus 1.10 [0.96-1.26] for PRS among heavy smokers with ≥ 40 pack-years of smoking) for moderate-to-severe COPD. Cross-ethnic portability of the PTRS was significantly higher than the PRS (paired t test p < 2.2 × 10-16 with portability gains ranging from 5% to 28%) for both dichotomous COPD traits and across all smoking strata. Our study demonstrates the value of PTRS for improved cross-ethnic portability compared to PRS in predicting COPD risk.
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Affiliation(s)
- Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pallavi P Balte
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Rajesh Kumar
- Division of Allergy and Clinical Immunology, Ann and Robert H. Lurie Children's Hospital, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Brian E Cade
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger A Metcalf
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Stacy Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shannon Dugan-Perez
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Laura R Loehr
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA 98101, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ramachandran S Vasan
- Boston University and the National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA 01702, USA; Department of Preventive Medicine and Epidemiology, School of Medicine and Public Health, Boston University, Boston, MA 02118, USA
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - George T O'Connor
- Pulmonary Center, Boston University, School of Medicine, Boston, MA 02118, USA
| | - Eugene Bleecker
- Department of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ravi Kalhan
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA 98109, USA
| | - Deborah Meyers
- Department of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Victor Ortega
- Pulmonary and Critical Care, School of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC 27709, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Elizabeth C Oelsner
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Heather E Wheeler
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | | | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.
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15
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Cornejo-Sanchez DM, Acharya A, Bharadwaj T, Marin-Gomez L, Pereira-Gomez P, Nouel-Saied LM, Nickerson DA, Bamshad MJ, Mefford HC, Schrauwen I, Carrizosa-Moog J, Cornejo-Ochoa W, Pineda-Trujillo N, Leal SM. SCN1A Variants as the Underlying Cause of Genetic Epilepsy with Febrile Seizures Plus in Two Multi-Generational Colombian Families. Genes (Basel) 2022; 13:754. [PMID: 35627139 PMCID: PMC9140479 DOI: 10.3390/genes13050754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic epilepsy with febrile seizures plus (GEFS+) is an autosomal dominant disorder with febrile or afebrile seizures that exhibits phenotypic variability. Only a few variants in SCN1A have been previously characterized for GEFS+, in Latin American populations where studies on the genetic and phenotypic spectrum of GEFS+ are scarce. We evaluated members in two multi-generational Colombian Paisa families whose affected members present with classic GEFS+. Exome and Sanger sequencing were used to detect the causal variants in these families. In each of these families, we identified variants in SCN1A causing GEFS+ with incomplete penetrance. In Family 047, we identified a heterozygous variant (c.3530C > G; p.(Pro1177Arg)) that segregates with GEFS+ in 15 affected individuals. In Family 167, we identified a previously unreported variant (c.725A > G; p.(Gln242Arg)) that segregates with the disease in a family with four affected members. Both variants are located in a cytoplasmic loop region in SCN1A and based on our findings the variants are classified as pathogenic and likely pathogenic, respectively. Our results expand the genotypic and phenotypic spectrum associated with SCN1A variants and will aid in improving molecular diagnostics and counseling in Latin American and other populations.
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Affiliation(s)
- Diana M. Cornejo-Sanchez
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; (D.M.C.-S.); (A.A.); (T.B.); (L.M.N.-S.); (I.S.)
- Gene Mapping Group, Faculty of Medicine, University of Antioquia, Medellin 050010470, Colombia; (L.M.-G.); (P.P.-G.); (J.C.-M.)
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; (D.M.C.-S.); (A.A.); (T.B.); (L.M.N.-S.); (I.S.)
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; (D.M.C.-S.); (A.A.); (T.B.); (L.M.N.-S.); (I.S.)
| | - Lizeth Marin-Gomez
- Gene Mapping Group, Faculty of Medicine, University of Antioquia, Medellin 050010470, Colombia; (L.M.-G.); (P.P.-G.); (J.C.-M.)
| | - Pilar Pereira-Gomez
- Gene Mapping Group, Faculty of Medicine, University of Antioquia, Medellin 050010470, Colombia; (L.M.-G.); (P.P.-G.); (J.C.-M.)
| | - Liz M. Nouel-Saied
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; (D.M.C.-S.); (A.A.); (T.B.); (L.M.N.-S.); (I.S.)
| | | | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; (UWCMG); (M.J.B.); (H.C.M.)
| | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; (UWCMG); (M.J.B.); (H.C.M.)
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Heather C. Mefford
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; (UWCMG); (M.J.B.); (H.C.M.)
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; (D.M.C.-S.); (A.A.); (T.B.); (L.M.N.-S.); (I.S.)
| | - Jaime Carrizosa-Moog
- Gene Mapping Group, Faculty of Medicine, University of Antioquia, Medellin 050010470, Colombia; (L.M.-G.); (P.P.-G.); (J.C.-M.)
| | - William Cornejo-Ochoa
- Pediatrics Group, Faculty of Medicine, University of Antioquia, Medellin 050010470, Colombia;
| | - Nicolas Pineda-Trujillo
- Gene Mapping Group, Faculty of Medicine, University of Antioquia, Medellin 050010470, Colombia; (L.M.-G.); (P.P.-G.); (J.C.-M.)
| | - Suzanne M. Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; (D.M.C.-S.); (A.A.); (T.B.); (L.M.N.-S.); (I.S.)
- Taub Institute for Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
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16
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Paredes MI, Lunn SM, Famulare M, Frisbie LA, Painter I, Burstein R, Roychoudhury P, Xie H, Mohamed Bakhash SA, Perez R, Lukes M, Ellis S, Sathees S, Mathias PC, Greninger A, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, McDermot E, Truong M, Nickerson DA, Bates DL, Hartman ME, Haugen E, Nguyen TN, Richards JD, Rodriguez JL, Stamatoyannopoulos JA, Thorland E, Melly G, Dykema PE, MacKellar DC, Gray HK, Singh A, Peterson JM, Russell D, Marcela Torres L, Lindquist S, Bedford T, Allen KJ, Oltean HN. Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study. Clin Infect Dis 2022; 75:e536-e544. [PMID: 35412591 PMCID: PMC9047245 DOI: 10.1093/cid/ciac279] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Indexed: 12/22/2022] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with 7 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Methods Our study includes individuals with positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) in the Washington Disease Reporting System with available viral genome data, from 1 December 2020 to 14 January 2022. The analysis was restricted to cases with specimens collected through sentinel surveillance. Using a Cox proportional hazards model with mixed effects, we estimated hazard ratios (HR) for hospitalization risk following infection with a variant, adjusting for age, sex, calendar week, and vaccination. Results In total, 58 848 cases were sequenced through sentinel surveillance, of which 1705 (2.9%) were hospitalized due to COVID-19. Higher hospitalization risk was found for infections with Gamma (HR 3.20, 95% confidence interval [CI] 2.40–4.26), Beta (HR 2.85, 95% CI 1.56–5.23), Delta (HR 2.28 95% CI 1.56–3.34), or Alpha (HR 1.64, 95% CI 1.29–2.07) compared to infections with ancestral lineages; Omicron (HR 0.92, 95% CI .56–1.52) showed no significant difference in risk. Following Alpha, Gamma, or Delta infection, unvaccinated patients show higher hospitalization risk, while vaccinated patients show no significant difference in risk, both compared to unvaccinated, ancestral lineage cases. Hospitalization risk following Omicron infection is lower with vaccination. Conclusions Infection with Alpha, Gamma, or Delta results in a higher hospitalization risk, with vaccination attenuating that risk. Our findings support hospital preparedness, vaccination, and genomic surveillance.
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Affiliation(s)
- Miguel I Paredes
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Michael Famulare
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA USA
| | | | - Ian Painter
- Washington State Department of Health, Shoreline, WA USA
| | - Roy Burstein
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Shah A Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Ricardo Perez
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Maria Lukes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sean Ellis
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Saraswathi Sathees
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Patrick C Mathias
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA USA
| | - Chris D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Weizhi Zhong
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
| | - Machiko Threlkeld
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Evan McDermot
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
| | - Melissa Truong
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA USA
| | - Daniel L Bates
- Altius Institute for Biomedical Sciences, Seattle, WA USA
| | - Matthew E Hartman
- Altius Institute for Biomedical Sciences, Seattle, WA USA.,Department of Cardiovascular Services, Swedish Medical Center, Seattle, WA USA
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, WA USA
| | | | | | | | | | - Eric Thorland
- Altius Institute for Biomedical Sciences, Seattle, WA USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA USA
| | | | | | - Hannah K Gray
- Washington State Department of Health, Shoreline, WA USA
| | - Avi Singh
- Washington State Department of Health, Shoreline, WA USA
| | | | - Denny Russell
- Washington State Department of Health, Shoreline, WA USA
| | | | | | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA USA
| | | | - Hanna N Oltean
- Washington State Department of Health, Shoreline, WA USA
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17
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Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genet Med 2022; 24:784-797. [PMID: 35148959 PMCID: PMC9119004 DOI: 10.1016/j.gim.2021.12.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS Over the past 10 years, the National Institutes of Health-supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.
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Affiliation(s)
- Samantha M Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT; Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ; Department of Genetics, Rutgers University, Piscataway, NJ
| | - Elizabeth E Blue
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Lisa H Chadwick
- Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD
| | - Zeynep H Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Kimberly F Doheny
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Colleen P Davis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Genetics, Yale School of Medicine, New Haven, CT
| | | | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA.
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA.
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18
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Pitsava G, Feldkamp ML, Pankratz N, Lane J, Kay DM, Conway KM, Hobbs C, Shaw GM, Reefhuis J, Jenkins MM, Almli LM, Moore C, Werler M, Browne ML, Cunniff C, Olshan AF, Pangilinan F, Brody LC, Sicko RJ, Finnell RH, Bamshad MJ, McGoldrick D, Nickerson DA, Mullikin JC, Romitti PA, Mills JL. Exome sequencing identifies variants in infants with sacral agenesis. Birth Defects Res 2022; 114:215-227. [PMID: 35274497 PMCID: PMC9338687 DOI: 10.1002/bdr2.1987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/22/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Sacral agenesis (SA) consists of partial or complete absence of the caudal end of the spine and often presents with additional birth defects. Several studies have examined gene variants for syndromic forms of SA, but only one has examined exomes of children with non-syndromic SA. METHODS Using buccal cell specimens from families of children with non-syndromic SA, exomes of 28 child-parent trios (eight with and 20 without a maternal diagnosis of pregestational diabetes) and two child-father duos (neither with diagnosis of maternal pregestational diabetes) were exome sequenced. RESULTS Three children had heterozygous missense variants in ID1 (Inhibitor of DNA Binding 1), with CADD scores >20 (top 1% of deleterious variants in the genome); two children inherited the variant from their fathers and one from the child's mother. Rare missense variants were also detected in PDZD2 (PDZ Domain Containing 2; N = 1) and SPTBN5 (Spectrin Beta, Non-erythrocytic 5; N = 2), two genes previously suggested to be associated with SA etiology. Examination of variants with autosomal recessive and X-linked recessive inheritance identified five and two missense variants, respectively. Compound heterozygous variants were identified in several genes. In addition, 12 de novo variants were identified, all in different genes in different children. CONCLUSIONS To our knowledge, this is the first study reporting a possible association between ID1 and non-syndromic SA. Although maternal pregestational diabetes has been strongly associated with SA, the missense variants in ID1 identified in two of three children were paternally inherited. These findings add to the knowledge of gene variants associated with non-syndromic SA and provide data for future studies.
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Affiliation(s)
- Georgia Pitsava
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcia L. Feldkamp
- Division of Medical Genetics, Department of Pediatrics, 295 Chipeta Way, Suite 2S010, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Denise M. Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kristin M. Conway
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, California, USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Jennita Reefhuis
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mary M. Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lynn M. Almli
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cynthia Moore
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Martha Werler
- Slone Epidemiology Center at Boston University, Boston, MA
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA
| | - Marilyn L. Browne
- New York State Department of Health, Birth Defects Registry, Albany, New York, USA
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, New York, USA
| | - Chris Cunniff
- Department of Pediatrics, Weill Cornell Medical College, New York, NY, USA
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Faith Pangilinan
- Gene and Environment Interaction Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Lawrence C. Brody
- Gene and Environment Interaction Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Robert J. Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Richard H. Finnell
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Michael J. Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Daniel McGoldrick
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James C. Mullikin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - James L. Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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19
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Gaedigk A, Boone EC, Scherer SE, Lee SB, Numanagić I, Sahinalp C, Smith JD, McGee S, Radhakrishnan A, Qin X, Wang WY, Farrow EG, Gonzaludo N, Halpern AL, Nickerson DA, Miller NA, Pratt VM, Kalman LV. CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project. J Mol Diagn 2022; 24:337-350. [PMID: 35134542 PMCID: PMC9069873 DOI: 10.1016/j.jmoldx.2021.12.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/09/2021] [Accepted: 12/28/2021] [Indexed: 01/13/2023] Open
Abstract
Pharmacogenetic tests typically target selected sequence variants to identify haplotypes that are often defined by star (∗) allele nomenclature. Due to their design, these targeted genotyping assays are unable to detect novel variants that may change the function of the gene product and thereby affect phenotype prediction and patient care. In the current study, 137 DNA samples that were previously characterized by the Genetic Testing Reference Material (GeT-RM) program using a variety of targeted genotyping methods were recharacterized using targeted and whole genome sequencing analysis. Sequence data were analyzed using three genotype calling tools to identify star allele diplotypes for CYP2C8, CYP2C9, and CYP2C19. The genotype calls from next-generation sequencing (NGS) correlated well to those previously reported, except when novel alleles were present in a sample. Six novel alleles and 38 novel suballeles were identified in the three genes due to identification of variants not covered by targeted genotyping assays. In addition, several ambiguous genotype calls from a previous study were resolved using the NGS and/or long-read NGS data. Diplotype calls were mostly consistent between the calling algorithms, although several discrepancies were noted. This study highlights the utility of NGS for pharmacogenetic testing and demonstrates that there are many novel alleles that are yet to be discovered, even in highly characterized genes such as CYP2C9 and CYP2C19.
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Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri
| | - Steven E Scherer
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Seung-Been Lee
- Precision Medicine Institute, Macrogen Inc., Seongnam, Republic of Korea
| | - Ibrahim Numanagić
- Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada
| | - Cenk Sahinalp
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Sean McGee
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | | | - Xiang Qin
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Wendy Y Wang
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri
| | - Emily G Farrow
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri; Center for Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri
| | - Nina Gonzaludo
- Medical Genomics Research, Illumina Inc., San Diego, California
| | - Aaron L Halpern
- Medical Genomics Research, Illumina Inc., San Diego, California
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Neil A Miller
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri; Center for Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lisa V Kalman
- Informatics and Data Science Branch, Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
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20
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Sajuthi SP, Everman JL, Jackson ND, Saef B, Rios CL, Moore CM, Mak ACY, Eng C, Fairbanks-Mahnke A, Salazar S, Elhawary J, Huntsman S, Medina V, Nickerson DA, Germer S, Zody MC, Abecasis G, Kang HM, Rice KM, Kumar R, Zaitlen NA, Oh S, Rodríguez-Santana J, Burchard EG, Seibold MA. Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology. Nat Commun 2022; 13:1632. [PMID: 35347136 PMCID: PMC8960819 DOI: 10.1038/s41467-022-28973-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
To identify genetic determinants of airway dysfunction, we performed a transcriptome-wide association study for asthma by combining RNA-seq data from the nasal airway epithelium of 681 children, with UK Biobank genetic association data. Our airway analysis identified 95 asthma genes, 58 of which were not identified by transcriptome-wide association analyses using other asthma-relevant tissues. Among these genes were MUC5AC, an airway mucin, and FOXA3, a transcriptional driver of mucus metaplasia. Muco-ciliary epithelial cultures from genotyped donors revealed that the MUC5AC risk variant increases MUC5AC protein secretion and mucus secretory cell frequency. Airway transcriptome-wide association analyses for mucus production and chronic cough also identified MUC5AC. These cis-expression variants were associated with trans effects on expression; the MUC5AC variant was associated with upregulation of non-inflammatory mucus secretory network genes, while the FOXA3 variant was associated with upregulation of type-2 inflammation-induced mucus-metaplasia pathway genes. Our results reveal genetic mechanisms of airway mucus pathobiology.
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Affiliation(s)
- Satria P Sajuthi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Benjamin Saef
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Cydney L Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Camille M Moore
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Biomedical Research, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Denver, CO, USA
| | - Angel C Y Mak
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Ana Fairbanks-Mahnke
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Sandra Salazar
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Jennifer Elhawary
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hyun Min Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Noah A Zaitlen
- Department of Neurology and Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Sam Oh
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | | | - Esteban G Burchard
- Department of Medicine, University of California-San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
- Department of Pediatrics, National Jewish Health, Denver, CO, USA.
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA.
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21
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Chau AS, Cole BL, Debley JS, Nanda K, Rosen ABI, Bamshad MJ, Nickerson DA, Torgerson TR, Allenspach EJ. Correction to: Heme oxygenase-1 deficiency presenting with interstitial lung disease and hemophagocytic flares. Pediatr Rheumatol Online J 2022; 20:19. [PMID: 35287710 PMCID: PMC8922765 DOI: 10.1186/s12969-021-00661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Alice S. Chau
- grid.34477.330000000122986657Division of Allergy & Infectious Disease, Department of Medicine, University of Washington, Seattle, Washington USA ,grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA
| | - Bonnie L. Cole
- grid.34477.330000000122986657Department of Pathology and Laboratory Medicine, University of Washington, Seattle, Washington USA ,grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA
| | - Jason S. Debley
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
| | - Kabita Nanda
- grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
| | - Aaron B. I. Rosen
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA
| | - Michael J. Bamshad
- grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA ,grid.34477.330000000122986657Genome Sciences, University of Washington, Seattle, Washington USA
| | - Deborah A. Nickerson
- grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Genome Sciences, University of Washington, Seattle, Washington USA
| | - Troy R. Torgerson
- grid.507729.eExperimental Immunology, Allen Institute, Seattle, Washington USA
| | - Eric J. Allenspach
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA ,grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
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22
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Geyer RE, Kotnik JH, Lyon V, Brandstetter E, Zigman Suchsland M, Han PD, Graham C, Ilcisin M, Kim AE, Chu HY, Nickerson DA, Starita LM, Bedford T, Lutz B, Thompson MJ. Diagnostic Accuracy of an At-Home, Rapid Self-test for Influenza: Prospective Comparative Accuracy Study. JMIR Public Health Surveill 2022; 8:e28268. [PMID: 35191852 PMCID: PMC8905479 DOI: 10.2196/28268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 11/02/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) for influenza used by individuals at home could potentially expand access to testing and reduce the impact of influenza on health systems. Improving access to testing could lead to earlier diagnosis following symptom onset, allowing more rapid interventions for those who test positive, including behavioral changes to minimize spread. However, the accuracy of RDTs for influenza has not been determined in self-testing populations. Objective This study aims to assess the accuracy of an influenza RDT conducted at home by lay users with acute respiratory illness compared with that of a self-collected sample by the same individual mailed to a laboratory for reference testing. Methods We conducted a comparative accuracy study of an at-home influenza RDT (Ellume) in a convenience sample of individuals experiencing acute respiratory illness symptoms. Participants were enrolled in February and March 2020 from the Greater Seattle region in Washington, United States. Participants were mailed the influenza RDT and reference sample collection materials, which they completed and returned for quantitative reverse-transcription polymerase chain reaction influenza testing in a central laboratory. We explored the impact of age, influenza type, duration, and severity of symptoms on RDT accuracy and on cycle threshold for influenza virus and ribonuclease P, a marker of human DNA. Results A total of 605 participants completed all study steps and were included in our analysis, of whom 87 (14.4%) tested positive for influenza by quantitative reverse-transcription polymerase chain reaction (70/87, 80% for influenza A and 17/87, 20% for influenza B). The overall sensitivity and specificity of the RDT compared with the reference test were 61% (95% CI 50%-71%) and 95% (95% CI 93%-97%), respectively. Among individuals with symptom onset ≤72 hours, sensitivity was 63% (95% CI 48%-76%) and specificity was 94% (95% CI 91%-97%), whereas, for those with duration >72 hours, sensitivity and specificity were 58% (95% CI 41%-74%) and 96% (95% CI 93%-98%), respectively. Viral load on reference swabs was negatively correlated with symptom onset, and quantities of the endogenous marker gene ribonuclease P did not differ among reference standard positive and negative groups, age groups, or influenza subtypes. The RDT did not have higher sensitivity or specificity among those who reported more severe illnesses. Conclusions The sensitivity and specificity of the self-test were comparable with those of influenza RDTs used in clinical settings. False-negative self-test results were more common when the test was used after 72 hours of symptom onset but were not related to inadequate swab collection or severity of illness. Therefore, the deployment of home tests may provide a valuable tool to support the management of influenza and other respiratory infections.
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Affiliation(s)
- Rachel E Geyer
- Department of Family Medicine, University of Washington, Seattle, WA, United States
| | - Jack Henry Kotnik
- Department of Family Medicine, University of Washington, Seattle, WA, United States.,Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Victoria Lyon
- Department of Family Medicine, University of Washington, Seattle, WA, United States
| | - Elisabeth Brandstetter
- Department of Medicine, University of Washington, Seattle, WA, United States.,Brotman Baty Institute, University of Washington, Seattle, WA, United States
| | | | - Peter D Han
- Brotman Baty Institute, University of Washington, Seattle, WA, United States.,Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Chelsey Graham
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Ashley E Kim
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA, United States.,Brotman Baty Institute, University of Washington, Seattle, WA, United States
| | - Deborah A Nickerson
- Brotman Baty Institute, University of Washington, Seattle, WA, United States.,Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Lea M Starita
- Brotman Baty Institute, University of Washington, Seattle, WA, United States.,Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Trevor Bedford
- Brotman Baty Institute, University of Washington, Seattle, WA, United States.,Department of Genome Sciences, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Barry Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, United States.,Brotman Baty Institute, University of Washington, Seattle, WA, United States
| | - Matthew J Thompson
- Department of Family Medicine, University of Washington, Seattle, WA, United States
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23
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Little A, Hu Y, Sun Q, Jain D, Broome J, Chen MH, Thibord F, McHugh C, Surendran P, Blackwell TW, Brody JA, Bhan A, Chami N, de Vries PS, Ekunwe L, Heard-Costa N, Hobbs BD, Manichaikul A, Moon JY, Preuss MH, Ryan K, Wang Z, Wheeler M, Yanek LR, Abecasis GR, Almasy L, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Choquet H, Correa A, Curran JE, Faraday N, Fornage M, Glahn DC, Hou L, Jorgenson E, Kooperberg C, Lewis JP, Lloyd-Jones DM, Loos RJF, Min YI, Mitchell BD, Morrison AC, Nickerson DA, North KE, O'Connell JR, Pankratz N, Psaty BM, Vasan RS, Rich SS, Rotter JI, Smith AV, Smith NL, Tang H, Tracy RP, Conomos MP, Laurie CA, Mathias RA, Li Y, Auer PL, Thornton T, Reiner AP, Johnson AD, Raffield LM. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative. Hum Mol Genet 2022; 31:347-361. [PMID: 34553764 PMCID: PMC8825339 DOI: 10.1093/hmg/ddab252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022] Open
Abstract
Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.
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Affiliation(s)
- Amarise Little
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Caitlin McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | | | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Paul S de Vries
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nancy Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ani Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yuan-I Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
- Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
- Department of Veterans Affairs Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, WA 98108, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT 05446, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | | | - Timothy Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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24
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Taub MA, Conomos MP, Keener R, Iyer KR, Weinstock JS, Yanek LR, Lane J, Miller-Fleming TW, Brody JA, Raffield LM, McHugh CP, Jain D, Gogarten SM, Laurie CA, Keramati A, Arvanitis M, Smith AV, Heavner B, Barwick L, Becker LC, Bis JC, Blangero J, Bleecker ER, Burchard EG, Celedón JC, Chang YPC, Custer B, Darbar D, de las Fuentes L, DeMeo DL, Freedman BI, Garrett ME, Gladwin MT, Heckbert SR, Hidalgo BA, Irvin MR, Islam T, Johnson WC, Kaab S, Launer L, Lee J, Liu S, Moscati A, North KE, Peyser PA, Rafaels N, Seidman C, Weeks DE, Wen F, Wheeler MM, Williams LK, Yang IV, Zhao W, Aslibekyan S, Auer PL, Bowden DW, Cade BE, Chen Z, Cho MH, Cupples LA, Curran JE, Daya M, Deka R, Eng C, Fingerlin TE, Guo X, Hou L, Hwang SJ, Johnsen JM, Kenny EE, Levin AM, Liu C, Minster RL, Naseri T, Nouraie M, Reupena MS, Sabino EC, Smith JA, Smith NL, Lasky-Su J, Taylor JG, Telen MJ, Tiwari HK, Tracy RP, White MJ, Zhang Y, Wiggins KL, Weiss ST, Vasan RS, Taylor KD, Sinner MF, Silverman EK, Shoemaker MB, Sheu WHH, Sciurba F, Schwartz DA, Rotter JI, Roden D, Redline S, Raby BA, Psaty BM, Peralta JM, Palmer ND, Nekhai S, Montgomery CG, Mitchell BD, Meyers DA, McGarvey ST, Mak AC, Loos RJ, Kumar R, Kooperberg C, Konkle BA, Kelly S, Kardia SL, Kaplan R, He J, Gui H, Gilliland FD, Gelb BD, Fornage M, Ellinor PT, de Andrade M, Correa A, Chen YDI, Boerwinkle E, Barnes KC, Ashley-Koch AE, Arnett DK, Albert C, Laurie CC, Abecasis G, Nickerson DA, Wilson JG, Rich SS, Levy D, Ruczinski I, Aviv A, Blackwell TW, Thornton T, O’Connell J, Cox NJ, Perry JA, Armanios M, Battle A, Pankratz N, Reiner AP, Mathias RA. Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed. Cell Genom 2022; 2:S2666-979X(21)00105-1. [PMID: 35530816 PMCID: PMC9075703 DOI: 10.1016/j.xgen.2021.100084] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 09/03/2021] [Accepted: 12/10/2021] [Indexed: 01/16/2023]
Abstract
Genetic studies on telomere length are important for understanding age-related diseases. Prior GWAS for leukocyte TL have been limited to European and Asian populations. Here, we report the first sequencing-based association study for TL across ancestrally-diverse individuals (European, African, Asian and Hispanic/Latino) from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. We used whole genome sequencing (WGS) of whole blood for variant genotype calling and the bioinformatic estimation of telomere length in n=109,122 individuals. We identified 59 sentinel variants (p-value <5×10-9) in 36 loci associated with telomere length, including 20 newly associated loci (13 were replicated in external datasets). There was little evidence of effect size heterogeneity across populations. Fine-mapping at OBFC1 indicated the independent signals colocalized with cell-type specific eQTLs for OBFC1 (STN1). Using a multi-variant gene-based approach, we identified two genes newly implicated in telomere length, DCLRE1B (SNM1B) and PARN. In PheWAS, we demonstrated our TL polygenic trait scores (PTS) were associated with increased risk of cancer-related phenotypes.
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Affiliation(s)
- Margaret A. Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matthew P. Conomos
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, MD, USA
| | - Kruthika R. Iyer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joshua S. Weinstock
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Lisa R. Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Lane
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Tyne W. Miller-Fleming
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin P. McHugh
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Stephanie M. Gogarten
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Cecelia A. Laurie
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Ali Keramati
- Department of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marios Arvanitis
- Department of Medicine, Division of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Albert V. Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Benjamin Heavner
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Lucas Barwick
- LTRC Data Coordinating Center, The Emmes Company, LLC, Rockville, MD, USA
| | - Lewis C. Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eugene R. Bleecker
- Department of Medicine, Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ, USA
- Division of Pharmacogenomics, University of Arizona, Tucson, AZ, USA
| | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yen Pei C. Chang
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Lisa de las Fuentes
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Melanie E. Garrett
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Mark T. Gladwin
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Bertha A. Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Talat Islam
- Division of Environmental Health, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - W. Craig Johnson
- Department of Biostatistics, Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, USA
| | - Stefan Kaab
- Department of Medicine I, University Hospital Munich, Ludwig-Maximilian’s University, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Lenore Launer
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jiwon Lee
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
| | - Simin Liu
- Department of Epidemiology and Brown Center for Global Cardiometabolic Health, Brown University, Providence, RI, USA
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Patricia A. Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Nicholas Rafaels
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | | | - Daniel E. Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Fayun Wen
- Center for Sickle Cell Disease and Department of Medicine, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Marsha M. Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Ivana V. Yang
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul L. Auer
- Zilber School of Public Health, University of Wisconsin, Milwaukee, Milwaukee, WI, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Brian E. Cade
- Harvard Medical School, Boston, MA, USA
- Division of Sleep Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Zhanghua Chen
- Division of Environmental Health, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- The National Heart, Lung, and Blood Institute, Boston University’s Framingham Heart Study, Framingham, MA, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Michelle Daya
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Ranjan Deka
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tasha E. Fingerlin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Denver, Aurora, CO, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Shih-Jen Hwang
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jill M. Johnsen
- Bloodworks Northwest Research Institute, Seattle, WA, USA
- University of Washington, Department of Medicine, Seattle, WA, USA
| | - Eimear E. Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Albert M. Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Chunyu Liu
- The National Heart, Lung, and Blood Institute, Boston University’s Framingham Heart Study, Framingham, MA, USA
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Ryan L. Minster
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
- Department of Epidemiology & International Health Institute, School of Public Health, Brown University, Providence, RI, USA
| | - Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Ester C. Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jennifer A. Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Nicholas L. Smith
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - James G. Taylor
- Center for Sickle Cell Disease and Department of Medicine, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Marilyn J. Telen
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
- Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
| | - Hemant K. Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Russell P. Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larrner College of Medicine, University of Vermont, Colchester, VT, USA
| | - Marquitta J. White
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ramachandran S. Vasan
- The National Heart, Lung, and Blood Institute, Boston University’s Framingham Heart Study, Framingham, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Moritz F. Sinner
- Department of Medicine I, University Hospital Munich, Ludwig-Maximilian’s University, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - M. Benjamin Shoemaker
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wayne H.-H. Sheu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Frank Sciurba
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A. Schwartz
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Daniel Roden
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Susan Redline
- Division of Sleep Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Benjamin A. Raby
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA
| | - Juan M. Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Sergei Nekhai
- Center for Sickle Cell Disease and Department of Medicine, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Courtney G. Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Deborah A. Meyers
- Department of Medicine, Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ, USA
- Division of Pharmacogenomics, University of Arizona, Tucson, AZ, USA
| | - Stephen T. McGarvey
- Department of Epidemiology & International Health Institute, School of Public Health, Brown University, Providence, RI, USA
| | | | - Angel C.Y. Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajesh Kumar
- Division of Allergy and Clinical Immunology, The Ann and Robert H. Lurie Children’s Hospital of Chicago, and Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Barbara A. Konkle
- Bloodworks Northwest Research Institute, Seattle, WA, USA
- University of Washington, Department of Medicine, Seattle, WA, USA
| | - Shannon Kelly
- Vitalant Research Institute, San Francisco, CA, USA
- UCSF Benioff Children’s Hospital, Oakland, CA, USA
| | - Sharon L.R. Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jiang He
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Frank D. Gilliland
- Division of Environmental Health, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute, Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Patrick T. Ellinor
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Adolfo Correa
- Jackson Heart Study and Departments of Medicine and Population Health Science, Jackson, MS, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kathleen C. Barnes
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Allison E. Ashley-Koch
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Donna K. Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Christine Albert
- Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | | | | | - Cathy C. Laurie
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | | | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MI, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Daniel Levy
- The National Heart, Lung, and Blood Institute, Boston University’s Framingham Heart Study, Framingham, MA, USA
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abraham Aviv
- Center of Human Development and Aging, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Timothy Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jeff O’Connell
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nancy J. Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James A. Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mary Armanios
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, MD, USA
- Departments of Computer Science and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Rasika A. Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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25
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Emanuels A, Heimonen J, O’Hanlon J, Kim AE, Wilcox N, McCulloch DJ, Brandstetter E, Wolf CR, Logue JK, Han PD, Pfau B, Newman KL, Hughes JP, Jackson ML, Uyeki TM, Boeckh M, Starita LM, Nickerson DA, Bedford T, Englund JA, Chu HY. Remote Household Observation for Noninfluenza Respiratory Viral Illness. Clin Infect Dis 2021; 73:e4411-e4418. [PMID: 33197930 PMCID: PMC7717193 DOI: 10.1093/cid/ciaa1719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Noninfluenza respiratory viruses are responsible for a substantial burden of disease in the United States. Household transmission is thought to contribute significantly to subsequent transmission through the broader community. In the context of the coronavirus disease 2019 (COVID-19) pandemic, contactless surveillance methods are of particular importance. METHODS From November 2019 to April 2020, 303 households in the Seattle area were remotely monitored in a prospective longitudinal study for symptoms of respiratory viral illness. Enrolled participants reported weekly symptoms and submitted respiratory samples by mail in the event of an acute respiratory illness (ARI). Specimens were tested for 14 viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using reverse-transcription polymerase chain reaction. Participants completed all study procedures at home without physical contact with research staff. RESULTS In total, 1171 unique participants in 303 households were monitored for ARI. Of participating households, 128 (42%) included a child aged <5 years and 202 (67%) included a child aged 5-12 years. Of the 678 swabs collected during the surveillance period, 237 (35%) tested positive for 1 or more noninfluenza respiratory viruses. Rhinovirus, common human coronaviruses, and respiratory syncytial virus were the most common. Four cases of SARS-CoV-2 were detected in 3 households. CONCLUSIONS This study highlights the circulation of respiratory viruses within households during the winter months during the emergence of the SARS-CoV-2 pandemic. Contactless methods of recruitment, enrollment, and sample collection were utilized throughout this study and demonstrate the feasibility of home-based, remote monitoring for respiratory infections.
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Affiliation(s)
- Anne Emanuels
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica Heimonen
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica O’Hanlon
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ashley E Kim
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Naomi Wilcox
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Denise J McCulloch
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter D Han
- Brotman Baty Institute, Seattle, Washington, USA
| | - Brian Pfau
- Brotman Baty Institute, Seattle, Washington, USA
| | - Kira L Newman
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - Timothy M Uyeki
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lea M Starita
- Brotman Baty Institute, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Brotman Baty Institute, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Janet A Englund
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
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26
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Weil AA, Sohlberg SL, O’Hanlon JA, Casto AM, Emanuels AW, Lo NK, Greismer EP, Magedson AM, Wilcox NC, Kim AE, Back L, Frazar CD, Pelle B, Sibley TR, Ilcisin M, Lee J, Ryke EL, Craft JC, Schwabe-Fry KM, Fay KA, Cho S, Han PD, Heidl SJ, Pfau BA, Truong M, Zhong W, Srivatsan SR, Harb KF, Gottlieb GS, Hughes JP, Nickerson DA, Lockwood CM, Starita LM, Bedford T, Shendure JA, Chu HY. SARS-CoV-2 Epidemiology on a Public University Campus in Washington State. Open Forum Infect Dis 2021; 8:ofab464. [PMID: 34805425 PMCID: PMC8599730 DOI: 10.1093/ofid/ofab464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/10/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND We aimed to evaluate a testing program to facilitate control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission at a large university and measure spread in the university community using viral genome sequencing. METHODS Our prospective longitudinal study used remote contactless enrollment, daily mobile symptom and exposure tracking, and self-swab sample collection. Individuals were tested if the participant was exposed to a known SARS-CoV-2-infected person, developed new symptoms, or reported high-risk behavior (such as attending an indoor gathering without masking or social distancing), if a member of a group experiencing an outbreak, or at enrollment. Study participants included students, staff, and faculty at an urban public university during the Autumn quarter of 2020. RESULTS We enrolled 16 476 individuals, performed 29 783 SARS-CoV-2 tests, and detected 236 infections. Seventy-five percent of positive cases reported at least 1 of the following: symptoms (60.8%), exposure (34.7%), or high-risk behaviors (21.5%). Greek community affiliation was the strongest risk factor for testing positive, and molecular epidemiology results suggest that specific large gatherings were responsible for several outbreaks. CONCLUSIONS A testing program focused on individuals with symptoms and unvaccinated persons who participate in large campus gatherings may be effective as part of a comprehensive university-wide mitigation strategy to control the spread of SARS-CoV-2.
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Affiliation(s)
- Ana A Weil
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Sarah L Sohlberg
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica A O’Hanlon
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amanda M Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Anne W Emanuels
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Natalie K Lo
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Emily P Greismer
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ariana M Magedson
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Naomi C Wilcox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ashley E Kim
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lewis Back
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Christian D Frazar
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ben Pelle
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Thomas R Sibley
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Misja Ilcisin
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Erica L Ryke
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - J Chris Craft
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | | | - Kairsten A Fay
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Shari Cho
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Peter D Han
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Sarah J Heidl
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Brian A Pfau
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Weizhi Zhong
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Katia F Harb
- Department of Environmental Health and Safety, University of Washington, Seattle, Washington, USA
| | - Geoffrey S Gottlieb
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Environmental Health and Safety, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Christina M Lockwood
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Jay A Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
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27
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Hirsch SD, Elling CL, Bootpetch TC, Scholes MA, Hafrén L, Streubel SO, Pine HS, Wine TM, Szeremeta W, Prager JD, Einarsdottir E, Yousaf A, Baschal EE, Rehman S, Bamshad MJ, Nickerson DA, Riazuddin S, Leal SM, Ahmed ZM, Yoon PJ, Kere J, Chan KH, Mattila PS, Friedman NR, Chonmaitree T, Frank DN, Ryan AF, Santos-Cortez RLP. The role of CDHR3 in susceptibility to otitis media. J Mol Med (Berl) 2021; 99:1571-1583. [PMID: 34322716 PMCID: PMC8541908 DOI: 10.1007/s00109-021-02118-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022]
Abstract
Otitis media (OM) is common in young children and can cause hearing loss and speech, language, and developmental delays. OM has high heritability; however, little is known about OM-related molecular and genetic processes. CDHR3 was previously identified as a locus for OM susceptibility, but to date, studies have focused on how the CDHR3 p.Cys529Tyr variant increases epithelial binding of rhinovirus-C and risk for lung or sinus pathology. In order to further delineate a role for CDHR3 in OM, we performed the following: exome sequencing using DNA samples from OM-affected individuals from 257 multi-ethnic families; Sanger sequencing, logistic regression and transmission disequilibrium tests for 407 US trios or probands with OM; 16S rRNA sequencing and analysis for middle ear and nasopharyngeal samples; and single-cell RNA sequencing and differential expression analyses for mouse middle ear. From exome sequence data, we identified a novel pathogenic CDHR3 splice variant that co-segregates with OM in US and Finnish families. Additionally, a frameshift and six missense rare or low-frequency variants were identified in Finnish probands. In US probands, the CDHR3 p.Cys529Tyr variant was associated with the absence of middle ear fluid at surgery and also with increased relative abundance of Lysobacter in the nasopharynx and Streptomyces in the middle ear. Consistent with published data on airway epithelial cells and our RNA-sequence data from human middle ear tissues, Cdhr3 expression is restricted to ciliated epithelial cells of the middle ear and is downregulated after acute OM. Overall, these findings suggest a critical role for CDHR3 in OM susceptibility. KEY MESSAGES: • Novel rare or low-frequency CDHR3 variants putatively confer risk for otitis media. • Pathogenic variant CDHR3 c.1653 + 3G > A was found in nine families with otitis media. • CDHR3 p.Cys529Tyr was associated with lack of effusion and bacterial otopathogens. • Cdhr3 expression was limited to ciliated epithelial cells in mouse middle ear. • Cdhr3 was downregulated 3 h after infection of mouse middle ear.
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Affiliation(s)
- Scott D Hirsch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
| | - Christina L Elling
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
| | - Tori C Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
| | - Melissa A Scholes
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado (CHCO), 13123 E. 16th Ave, Aurora, CO, 80045, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Tukholmankatu 8A, 00290, Helsinki, Finland
| | - Sven-Olrik Streubel
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado (CHCO), 13123 E. 16th Ave, Aurora, CO, 80045, USA
| | - Harold S Pine
- Department of Otolaryngology, University of Texas Medical Branch (UTMB), 301 8th St, Galveston, TX, 77550, USA
| | - Todd M Wine
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado (CHCO), 13123 E. 16th Ave, Aurora, CO, 80045, USA
| | - Wasyl Szeremeta
- Department of Otolaryngology, University of Texas Medical Branch (UTMB), 301 8th St, Galveston, TX, 77550, USA
| | - Jeremy D Prager
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado (CHCO), 13123 E. 16th Ave, Aurora, CO, 80045, USA
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, PO Box 63, Biomedicum 1, 3rd floor, Haartmaninkatu 8, 00014, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institute, 141 86, Huddinge, Stockholm, Sweden
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, 171 21, Solna, Sweden
| | - Ayesha Yousaf
- Bahauddin Zakariya University, Multan, 60000, Punjab, Pakistan
| | - Erin E Baschal
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
| | - Sakina Rehman
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, 670 West Baltimore St., Room 7181, Baltimore, MD, 21201, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave. NE, Seattle, WA, 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave. NE, Seattle, WA, 98195, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, 670 West Baltimore St., Room 7181, Baltimore, MD, 21201, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University, William Black Building, 650 West 168th St, New York, NY, 10032, USA
| | - Zubair M Ahmed
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, 670 West Baltimore St., Room 7181, Baltimore, MD, 21201, USA
| | - Patricia J Yoon
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado (CHCO), 13123 E. 16th Ave, Aurora, CO, 80045, USA
| | - Juha Kere
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, PO Box 63, Biomedicum 1, 3rd floor, Haartmaninkatu 8, 00014, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institute, 141 86, Huddinge, Stockholm, Sweden
| | - Kenny H Chan
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado (CHCO), 13123 E. 16th Ave, Aurora, CO, 80045, USA
| | - Petri S Mattila
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Tukholmankatu 8A, 00290, Helsinki, Finland
| | - Norman R Friedman
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA
- Department of Pediatric Otolaryngology, Children's Hospital Colorado (CHCO), 13123 E. 16th Ave, Aurora, CO, 80045, USA
| | - Tasnee Chonmaitree
- Division of Infectious Diseases, Department of Pediatrics, UTMB, 301 8th St, Galveston, TX, 77550, USA
| | - Daniel N Frank
- Division of Infectious Diseases, Department of Medicine, School of Medicine, CU-AMC, 12700 E. 19th Ave, Aurora, CO, 80045, USA
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, San Diego School of Medicine and Veterans Affairs Medical Center, University of California, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), 12700 E. 19th Ave, Aurora, CO, 80045, USA.
- Center for Children's Surgery, CHCO, 13123 E. 16th Ave, Aurora, CO, 80045, USA.
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Olson NC, Raffield LM, Moxley AH, Miller-Fleming TW, Auer PL, Franceschini N, Ngo D, Thornton TA, Lange EM, Li Y, Nickerson DA, Zakai NA, Gerszten RE, Cox NJ, Correa A, Mohlke KL, Reiner AP. Soluble Urokinase Plasminogen Activator Receptor: Genetic Variation and Cardiovascular Disease Risk in Blacks. Circ Genom Precis Med 2021; 14:e003421. [PMID: 34706549 DOI: 10.1161/circgen.121.003421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND suPAR (Soluble urokinase plasminogen activator receptor) has emerged as an important biomarker of coagulation, inflammation, and cardiovascular disease (CVD) risk. The contribution of suPAR to CVD risk and its genetic influence in the Black population have not been evaluated. METHODS We measured suPAR in 3492 Blacks from the prospective, community-based JHS (Jackson Heart Study). Cross-sectional associations of suPAR with lifestyle and CVD risk factors were assessed, whole-genome sequence data were used to evaluate genetic associations of suPAR, and relationships of suPAR with incident CVD outcomes and overall mortality were estimated over follow-up. RESULTS In Cox models adjusted for traditional CVD risk factors, estimated glomerular filtration rate, and CRP (C-reactive protein), each 1-SD higher suPAR was associated with a 21% to 31% increased risk of incident coronary heart disease, heart failure, stroke, and mortality. In the genome-wide association study, 2 missense (rs399145 encoding p.Thr86Ala, rs4760 encoding p.Phe272Leu) and 2 noncoding regulatory variants (rs73935023 within an enhancer element and rs4251805 within the promoter) of PLAUR on chromosome 19 were each independently associated with suPAR and together explained 14% of suPAR phenotypic variation. The allele frequencies of each of the four suPAR-associated genetic variants differ considerably across African and European populations. We further show that PLAUR rs73935023 can alter transcriptional activity in vitro. We did not find any association between genetically determined suPAR and CVD in JHS or a larger electronic medical record-based analyses of Blacks or Whites. CONCLUSIONS Our results demonstrate the importance of ancestry-differentiated genetic variation on suPAR levels and indicate suPAR is a CVD biomarker in Black adults.
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Affiliation(s)
- Nels C Olson
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington. (N.C.O., N.A.Z.)
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill. (L.M.R., A.H.M., Y.L., K.L.M.)
| | - Anne H Moxley
- Department of Genetics, University of North Carolina, Chapel Hill. (L.M.R., A.H.M., Y.L., K.L.M.)
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (T.W.M.-F., N.J.C.)
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee (P.L.A.)
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill. (N.F.)
| | - Debby Ngo
- Beth Israel Deaconess Medical Center, Boston, MA (D.N., R.E.G.)
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle. (T.A.T.)
| | - Ethan M Lange
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora (E.M.L.)
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill. (L.M.R., A.H.M., Y.L., K.L.M.).,Department of Biostatistics, University of North Carolina, Chapel Hill. (Y.L.).,Department of Computer Science, University of North Carolina, Chapel Hill. (Y.L.)
| | | | - Neil A Zakai
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington. (N.C.O., N.A.Z.).,Department of Medicine, Larner College of Medicine, University of Vermont, Burlington. (N.A.Z.)
| | | | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (T.W.M.-F., N.J.C.)
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson (A.C.)
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill. (L.M.R., A.H.M., Y.L., K.L.M.)
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle. (A.P.R.)
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29
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Tran TT, Keller RB, Guillemyn B, Pepin M, Corteville JE, Khatib S, Fallah MS, Zeinali S, Malfait F, Symoens S, Coucke P, Witters P, Levtchenko E, Bagherian H, Nickerson DA, Bamshad MJ, Chong JX, Byers PH. Biallelic variants in MESD, which encodes a WNT-signaling-related protein, in four new families with recessively inherited osteogenesis imperfecta. HGG Adv 2021; 2:100051. [PMID: 35047842 PMCID: PMC8756491 DOI: 10.1016/j.xhgg.2021.100051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/13/2021] [Indexed: 12/02/2022] Open
Abstract
The bone disorder osteogenesis imperfecta (OI) is genetically heterogeneous. Most affected individuals have an autosomal dominant disorder caused by heterozygous variants in either of the type I collagen genes (COL1A1 or COL1A2). To date, two reports have linked Mesoderm Development LRP Chaperone (MESD) to autosomal recessive OI type XX. Four different biallelic pathogenic variants in MESD were shown to cause a progressively deforming phenotype, associated with recurrent fractures and oligodontia in five individuals in five families. Recently, compound heterozygosity for a frameshift predicted to lead to a premature termination codon in exon 2 of the 3-exon gene and a second frameshift in the terminal exon in MESD were detected in three stillbirths in one family with severe OI consistent with the neonatal lethal phenotype. We have identified four additional individuals from four independent families with biallelic variants in MESD: the earlier reported c.632dupA (p.Lys212Glufs∗19) and c.676C>T (p.Arg226∗)-which are associated with a severe form of OI-and one new pathogenic variant, c.603-606delTAAA (p.Asn201Lysfs∗15), which causes a neonatal lethal form of OI. MESD acts in the WNT signaling pathway, where it is thought to play a role in the folding of the WNT co-receptors low-density lipoprotein receptor-related proteins 5 and 6 (LRP5/LRP6) and in chaperoning their transit to the cell surface. Our report broadens the phenotypic and genetic spectrum of MESD-related OI, provides additional insight into the pathogenic pathways, and underscores the necessity of MESD for normal WNT signaling in bone formation.
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Affiliation(s)
- Thao T. Tran
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Rachel B. Keller
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Brecht Guillemyn
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, Belgium
| | - Melanie Pepin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jane E. Corteville
- Department of Reproductive Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samir Khatib
- GMDC Al Quds University, P.O. Box 5100, Abu Dis, Palestine
| | | | - Sirous Zeinali
- Department of Medical Genetics, Kawsar Human Genetics Research Center, Tehran, Iran
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fransiska Malfait
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, Belgium
| | - Sofie Symoens
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, Belgium
| | - Peter Witters
- Center for Metabolic Diseases, University Hospital Leuven, Department of Paediatric Gastroenterology, Hepatology, and Nutrition, Leuven, Belgium
| | - Elena Levtchenko
- University Hospital Leuven, Departments of Pediatric Nephrology and Development and Regeneration, Leuven, Belgium
| | - Hamideh Bagherian
- GMDC Al Quds University, P.O. Box 5100, Abu Dis, Palestine
- Department of Medical Genetics, Kawsar Human Genetics Research Center, Tehran, Iran
| | | | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Jessica X. Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | | | - Peter H. Byers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
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30
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Mikhaylova AV, McHugh CP, Polfus LM, Raffield LM, Boorgula MP, Blackwell TW, Brody JA, Broome J, Chami N, Chen MH, Conomos MP, Cox C, Curran JE, Daya M, Ekunwe L, Glahn DC, Heard-Costa N, Highland HM, Hobbs BD, Ilboudo Y, Jain D, Lange LA, Miller-Fleming TW, Min N, Moon JY, Preuss MH, Rosen J, Ryan K, Smith AV, Sun Q, Surendran P, de Vries PS, Walter K, Wang Z, Wheeler M, Yanek LR, Zhong X, Abecasis GR, Almasy L, Barnes KC, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Chavan S, Cho MH, Choquet H, Correa A, Cox N, DeMeo DL, Faraday N, Fornage M, Gerszten RE, Hou L, Johnson AD, Jorgenson E, Kaplan R, Kooperberg C, Kundu K, Laurie CA, Lettre G, Lewis JP, Li B, Li Y, Lloyd-Jones DM, Loos RJF, Manichaikul A, Meyers DA, Mitchell BD, Morrison AC, Ngo D, Nickerson DA, Nongmaithem S, North KE, O'Connell JR, Ortega VE, Pankratz N, Perry JA, Psaty BM, Rich SS, Soranzo N, Rotter JI, Silverman EK, Smith NL, Tang H, Tracy RP, Thornton TA, Vasan RS, Zein J, Mathias RA, Reiner AP, Auer PL. Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:1836-1851. [PMID: 34582791 PMCID: PMC8546043 DOI: 10.1016/j.ajhg.2021.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.
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MESH Headings
- Asthma/epidemiology
- Asthma/genetics
- Asthma/metabolism
- Asthma/pathology
- Biomarkers/metabolism
- Dermatitis, Atopic/epidemiology
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/metabolism
- Dermatitis, Atopic/pathology
- Genetic Predisposition to Disease
- Genome, Human
- Genome-Wide Association Study
- Humans
- Leukocytes/pathology
- National Heart, Lung, and Blood Institute (U.S.)
- Phenotype
- Polymorphism, Single Nucleotide
- Prognosis
- Proteome/analysis
- Proteome/metabolism
- Pulmonary Disease, Chronic Obstructive/epidemiology
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/pathology
- Quantitative Trait Loci
- United Kingdom/epidemiology
- United States/epidemiology
- Whole Genome Sequencing
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Affiliation(s)
- Anna V Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Linda M Polfus
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Corey Cox
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA 02155, USA
| | - Nancy Heard-Costa
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yann Ilboudo
- Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Nancy Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Jonathon Rosen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xue Zhong
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Terri H Beaty
- School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nancy Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lifang Hou
- Institute for Public Health and Medicine, Northwestern University, Chicago, IL 60661, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Guillaume Lettre
- Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, and Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald M Lloyd-Jones
- Division of Cardiology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60661, USA; Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60661, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Debby Ngo
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Suraj Nongmaithem
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Victor E Ortega
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Department of Health Service, University of Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge CB1 8RN, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Department of Health Service, University of Washington, Seattle, WA 98105, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98105, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Department of Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT 05446, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA; Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | - Ramachandran S Vasan
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Joe Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexander P Reiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin, Milwaukee, Milwaukee, WI 53205, USA.
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Chung E, Chow EJ, Wilcox NC, Burstein R, Brandstetter E, Han PD, Fay K, Pfau B, Adler A, Lacombe K, Lockwood CM, Uyeki TM, Shendure J, Duchin JS, Rieder MJ, Nickerson DA, Boeckh M, Famulare M, Hughes JP, Starita LM, Bedford T, Englund JA, Chu HY. Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting. JAMA Pediatr 2021; 175:e212025. [PMID: 34115094 PMCID: PMC8491103 DOI: 10.1001/jamapediatrics.2021.2025] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023]
Abstract
Importance The association between COVID-19 symptoms and SARS-CoV-2 viral levels in children living in the community is not well understood. Objective To characterize symptoms of pediatric COVID-19 in the community and analyze the association between symptoms and SARS-CoV-2 RNA levels, as approximated by cycle threshold (Ct) values, in children and adults. Design, Setting, and Participants This cross-sectional study used a respiratory virus surveillance platform in persons of all ages to detect community COVID-19 cases from March 23 to November 9, 2020. A population-based convenience sample of children younger than 18 years and adults in King County, Washington, who enrolled online for home self-collection of upper respiratory samples for SARS-CoV-2 testing were included. Exposures Detection of SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) from participant-collected samples. Main Outcomes and Measures RT-PCR-confirmed SARS-CoV-2 infection, with Ct values stratified by age and symptoms. Results Among 555 SARS-CoV-2-positive participants (mean [SD] age, 33.7 [20.1] years; 320 were female [57.7%]), 47 of 123 children (38.2%) were asymptomatic compared with 31 of 432 adults (7.2%). When symptomatic, fewer symptoms were reported in children compared with adults (mean [SD], 1.6 [2.0] vs 4.5 [3.1]). Symptomatic individuals had lower Ct values (which corresponded to higher viral RNA levels) than asymptomatic individuals (adjusted estimate for children, -3.0; 95% CI, -5.5 to -0.6; P = .02; adjusted estimate for adults, -2.9; 95% CI, -5.2 to -0.6; P = .01). The difference in mean Ct values was neither statistically significant between symptomatic children and symptomatic adults (adjusted estimate, -0.7; 95% CI, -2.2 to 0.9; P = .41) nor between asymptomatic children and asymptomatic adults (adjusted estimate, -0.6; 95% CI, -4.0 to 2.8; P = .74). Conclusions and Relevance In this community-based cross-sectional study, SARS-CoV-2 RNA levels, as determined by Ct values, were significantly higher in symptomatic individuals than in asymptomatic individuals and no significant age-related differences were found. Further research is needed to understand the role of SARS-CoV-2 RNA levels and viral transmission.
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Affiliation(s)
- Erin Chung
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle
| | - Eric J. Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Naomi C. Wilcox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Roy Burstein
- Institute for Disease Modeling, Seattle, Washington
| | - Elisabeth Brandstetter
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle, Washington
| | | | - Christina M. Lockwood
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle
| | - Timothy M. Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
- Howard Hughes Medical Institute, Seattle, Washington
| | - Jeffrey S. Duchin
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Public Health—Seattle & King County, Seattle, Washington
| | - Mark J. Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Deborah A. Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Michael Boeckh
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
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32
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Jackson ML, Starita L, Kiniry E, Phillips CH, Wellwood S, Cho S, Kiavand A, Truong M, Han P, Richardson M, Wolf CR, Heimonen J, Nickerson DA, Chu HY. Incidence of Medically Attended Acute Respiratory Illnesses Due to Respiratory Viruses Across the Life Course During the 2018/19 Influenza Season. Clin Infect Dis 2021; 73:802-807. [PMID: 33590002 PMCID: PMC7929037 DOI: 10.1093/cid/ciab131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Indexed: 11/25/2022] Open
Abstract
Background While multiple respiratory viruses circulate in humans, few studies have compared the incidence of different viruses across the life course. We estimated the incidence of outpatient illness due to 12 different viruses during November 2018 through April 2019 in a fully enumerated population. Methods We conducted active surveillance for ambulatory care visits for acute respiratory illness (ARI) among members of Kaiser Permanente Washington (KPWA). Enrolled patients provided respiratory swab specimens which were tested for 12 respiratory viruses using RT-PCR. We estimated the cumulative incidence of infection due to each virus overall and by age group. Results The KPWA population under surveillance included 202,562 individuals, of whom 2,767 (1.4%) were enrolled in the study. Influenza A(H3N2) was the most commonly detected virus, with an overall incidence 21 medically attended illnesses per 1,000 population; the next most common viruses were influenza A(H1N1) (18 per 1,000), coronaviruses (13 per 1,000), respiratory syncytial virus (RSV, 13 per 1,000), and rhinovirus (9 per 1,000). RSV was the most common cause of medically attended ARI among children aged 1-4 years; coronaviruses were the most common among adults aged ≥65 years. Conclusions Consistent with other studies focused on single viruses, we found that influenza and RSV were major causes of acute respiratory illness in persons of all ages. In comparison, coronaviruses and rhinovirus were also important pathogens. Prior to the emergence of SARS-CoV-2, coronaviruses were the second-most common cause of medically attended ARI during the 2018/19 influenza season.
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Affiliation(s)
- Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, Washington, USA
| | - Lea Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Erika Kiniry
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, Washington, USA
| | - C Hallie Phillips
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, Washington, USA
| | - Stacie Wellwood
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, Washington, USA
| | - Shari Cho
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Anahita Kiavand
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Peter Han
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Matthew Richardson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica Heimonen
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
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33
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Cade BE, Lee J, Sofer T, Wang H, Zhang M, Chen H, Gharib SA, Gottlieb DJ, Guo X, Lane JM, Liang J, Lin X, Mei H, Patel SR, Purcell SM, Saxena R, Shah NA, Evans DS, Hanis CL, Hillman DR, Mukherjee S, Palmer LJ, Stone KL, Tranah GJ, Abecasis GR, Boerwinkle EA, Correa A, Cupples LA, Kaplan RC, Nickerson DA, North KE, Psaty BM, Rotter JI, Rich SS, Tracy RP, Vasan RS, Wilson JG, Zhu X, Redline S. Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program. Genome Med 2021; 13:136. [PMID: 34446064 PMCID: PMC8394596 DOI: 10.1186/s13073-021-00917-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/28/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Sleep-disordered breathing is a common disorder associated with significant morbidity. The genetic architecture of sleep-disordered breathing remains poorly understood. Through the NHLBI Trans-Omics for Precision Medicine (TOPMed) program, we performed the first whole-genome sequence analysis of sleep-disordered breathing. METHODS The study sample was comprised of 7988 individuals of diverse ancestry. Common-variant and pathway analyses included an additional 13,257 individuals. We examined five complementary traits describing different aspects of sleep-disordered breathing: the apnea-hypopnea index, average oxyhemoglobin desaturation per event, average and minimum oxyhemoglobin saturation across the sleep episode, and the percentage of sleep with oxyhemoglobin saturation < 90%. We adjusted for age, sex, BMI, study, and family structure using MMSKAT and EMMAX mixed linear model approaches. Additional bioinformatics analyses were performed with MetaXcan, GIGSEA, and ReMap. RESULTS We identified a multi-ethnic set-based rare-variant association (p = 3.48 × 10-8) on chromosome X with ARMCX3. Additional rare-variant associations include ARMCX3-AS1, MRPS33, and C16orf90. Novel common-variant loci were identified in the NRG1 and SLC45A2 regions, and previously associated loci in the IL18RAP and ATP2B4 regions were associated with novel phenotypes. Transcription factor binding site enrichment identified associations with genes implicated with respiratory and craniofacial traits. Additional analyses identified significantly associated pathways. CONCLUSIONS We have identified the first gene-based rare-variant associations with objectively measured sleep-disordered breathing traits. Our results increase the understanding of the genetic architecture of sleep-disordered breathing and highlight associations in genes that modulate lung development, inflammation, respiratory rhythmogenesis, and HIF1A-mediated hypoxic response.
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Affiliation(s)
- Brian E. Cade
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA
| | - Jiwon Lee
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA
| | - Tamar Sofer
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Heming Wang
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA
| | - Man Zhang
- grid.411024.20000 0001 2175 4264Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Han Chen
- grid.267308.80000 0000 9206 2401Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Sina A. Gharib
- grid.34477.330000000122986657Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA 98195 USA
| | - Daniel J. Gottlieb
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.410370.10000 0004 4657 1992VA Boston Healthcare System, Boston, MA 02132 USA
| | - Xiuqing Guo
- grid.239844.00000 0001 0157 6501The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Jacqueline M. Lane
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Jingjing Liang
- grid.67105.350000 0001 2164 3847Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Xihong Lin
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Hao Mei
- grid.410721.10000 0004 1937 0407Department of Data Science, University of Mississippi Medical Center, Jackson, MS 29216 USA
| | - Sanjay R. Patel
- grid.21925.3d0000 0004 1936 9000Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213 USA
| | - Shaun M. Purcell
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA
| | - Richa Saxena
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Neomi A. Shah
- grid.59734.3c0000 0001 0670 2351Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Daniel S. Evans
- grid.17866.3e0000000098234542California Pacific Medical Center Research Institute, San Francisco, CA 94107 USA
| | - Craig L. Hanis
- grid.267308.80000 0000 9206 2401Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - David R. Hillman
- grid.3521.50000 0004 0437 5942Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia 6009 Australia
| | - Sutapa Mukherjee
- Sleep Health Service, Respiratory and Sleep Services, Southern Adelaide Local Health Network, Adelaide, South Australia Australia ,grid.1014.40000 0004 0367 2697Adelaide Institute for Sleep Health, Flinders University, Adelaide, South Australia Australia
| | - Lyle J. Palmer
- grid.1010.00000 0004 1936 7304School of Public Health, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Katie L. Stone
- grid.17866.3e0000000098234542California Pacific Medical Center Research Institute, San Francisco, CA 94107 USA
| | - Gregory J. Tranah
- grid.17866.3e0000000098234542California Pacific Medical Center Research Institute, San Francisco, CA 94107 USA
| | | | - Gonçalo R. Abecasis
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Eric A. Boerwinkle
- grid.267308.80000 0000 9206 2401Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Adolfo Correa
- grid.410721.10000 0004 1937 0407Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216 USA ,Jackson Heart Study, Jackson, MS 39216 USA
| | - L. Adrienne Cupples
- grid.189504.10000 0004 1936 7558Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118 USA ,grid.510954.c0000 0004 0444 3861Framingham Heart Study, Framingham, MA 01702 USA
| | - Robert C. Kaplan
- grid.251993.50000000121791997Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, 10461 USA
| | - Deborah A. Nickerson
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA ,grid.34477.330000000122986657Northwest Genomics Center, Seattle, WA 98105 USA
| | - Kari E. North
- grid.410711.20000 0001 1034 1720Department of Epidemiology and Carolina Center of Genome Sciences, University of North Carolina, Chapel Hill, NC 27514 USA
| | - Bruce M. Psaty
- grid.34477.330000000122986657Cardiovascular Health Study, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA 98101 USA ,grid.488833.c0000 0004 0615 7519Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101 USA
| | - Jerome I. Rotter
- grid.239844.00000 0001 0157 6501The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Stephen S. Rich
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
| | - Russell P. Tracy
- grid.59062.380000 0004 1936 7689Department of Pathology, University of Vermont, Colchester, VT 05405 USA
| | - Ramachandran S. Vasan
- grid.510954.c0000 0004 0444 3861Framingham Heart Study, Framingham, MA 01702 USA ,grid.189504.10000 0004 1936 7558Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118 USA
| | - James G. Wilson
- grid.410721.10000 0004 1937 0407Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216 USA
| | - Xiaofeng Zhu
- grid.67105.350000 0001 2164 3847Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Susan Redline
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.239395.70000 0000 9011 8547Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
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34
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Pitsava G, Feldkamp ML, Pankratz N, Lane J, Kay DM, Conway KM, Shaw GM, Reefhuis J, Jenkins MM, Almli LM, Olshan AF, Pangilinan F, Brody LC, Sicko RJ, Hobbs CA, Bamshad M, McGoldrick D, Nickerson DA, Finnell RH, Mullikin J, Romitti PA, Mills JL. Exome sequencing of child-parent trios with bladder exstrophy: Findings in 26 children. Am J Med Genet A 2021; 185:3028-3041. [PMID: 34355505 DOI: 10.1002/ajmg.a.62439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/31/2021] [Accepted: 07/08/2021] [Indexed: 12/31/2022]
Abstract
Bladder exstrophy (BE) is a rare, lower ventral midline defect with the bladder and part of the urethra exposed. The etiology of BE is unknown but thought to be influenced by genetic variation with more recent studies suggesting a role for rare variants. As such, we conducted paired-end exome sequencing in 26 child/mother/father trios. Three children had rare (allele frequency ≤ 0.0001 in several public databases) inherited variants in TSPAN4, one with a loss-of-function variant and two with missense variants. Two children had loss-of-function variants in TUBE1. Four children had rare missense or nonsense variants (one per child) in WNT3, CRKL, MYH9, or LZTR1, genes previously associated with BE. We detected 17 de novo missense variants in 13 children and three de novo loss-of-function variants (AKR1C2, PRRX1, PPM1D) in three children (one per child). We also detected rare compound heterozygous loss-of-function variants in PLCH2 and CLEC4M and rare inherited missense or loss-of-function variants in additional genes applying autosomal recessive (three genes) and X-linked recessive inheritance models (13 genes). Variants in two genes identified may implicate disruption in cell migration (TUBE1) and adhesion (TSPAN4) processes, mechanisms proposed for BE, and provide additional evidence for rare variants in the development of this defect.
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Affiliation(s)
- Georgia Pitsava
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcia L Feldkamp
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kristin M Conway
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Jennita Reefhuis
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lynn M Almli
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Faith Pangilinan
- Gene and Environment Interaction Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Lawrence C Brody
- Gene and Environment Interaction Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Robert J Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Mike Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Daniel McGoldrick
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Richard H Finnell
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - James Mullikin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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35
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Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet 2021; 108:1436-1449. [PMID: 34216551 PMCID: PMC8387463 DOI: 10.1016/j.ajhg.2021.06.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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Affiliation(s)
- Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA.
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hailey Loucks
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Edith P Almanza Fuerte
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Catherine R Paschal
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jenny Thies
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - James T Bennett
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily S Bonkowski
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Zoe Nelson
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Audrey Squire
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Megan Sikes
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Erika Beckman
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dawn Earl
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Seth J Perlman
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, WA 98105, USA
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Anne V Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tara L Wenger
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Margaret P Adam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Angela Sun
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Christina Lam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Irene Chang
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Xue Zou
- Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Stephanie L Austin
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Erin Huggins
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Apoorva K Iyengar
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University; Durham, NC 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - William H Majoros
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Priya S Kishnani
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tim Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Developmental Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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Kundishora AJ, Peters ST, Pinard A, Duran D, Panchagnula S, Barak T, Miyagishima DF, Dong W, Smith H, Ocken J, Dunbar A, Nelson-Williams C, Haider S, Walker RL, Li B, Zhao H, Thumkeo D, Marlier A, Duy PQ, Diab NS, Reeves BC, Robert SM, Sujijantarat N, Stratman AN, Chen YH, Zhao S, Roszko I, Lu Q, Zhang B, Mane S, Castaldi C, López-Giráldez F, Knight JR, Bamshad MJ, Nickerson DA, Geschwind DH, Chen SSL, Storm PB, Diluna ML, Matouk CC, Orbach DB, Alper SL, Smith ER, Lifton RP, Gunel M, Milewicz DM, Jin SC, Kahle KT. DIAPH1 Variants in Non-East Asian Patients With Sporadic Moyamoya Disease. JAMA Neurol 2021; 78:993-1003. [PMID: 34125151 PMCID: PMC8204259 DOI: 10.1001/jamaneurol.2021.1681] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/31/2021] [Indexed: 12/18/2022]
Abstract
Importance Moyamoya disease (MMD), a progressive vasculopathy leading to narrowing and ultimate occlusion of the intracranial internal carotid arteries, is a cause of childhood stroke. The cause of MMD is poorly understood, but genetic factors play a role. Several familial forms of MMD have been identified, but the cause of most cases remains elusive, especially among non-East Asian individuals. Objective To assess whether ultrarare de novo and rare, damaging transmitted variants with large effect sizes are associated with MMD risk. Design, Setting, and Participants A genetic association study was conducted using whole-exome sequencing case-parent MMD trios in a small discovery cohort collected over 3.5 years (2016-2019); data were analyzed in 2020. Medical records from US hospitals spanning a range of 1 month to 1.5 years were reviewed for phenotyping. Exomes from a larger validation cohort were analyzed to identify additional rare, large-effect variants in the top candidate gene. Participants included patients with MMD and, when available, their parents. All participants who met criteria and were presented with the option to join the study agreed to do so; none were excluded. Twenty-four probands (22 trios and 2 singletons) composed the discovery cohort, and 84 probands (29 trios and 55 singletons) composed the validation cohort. Main Outcomes and Measures Gene variants were identified and filtered using stringent criteria. Enrichment and case-control tests assessed gene-level variant burden. In silico modeling estimated the probability of variant association with protein structure. Integrative genomics assessed expression patterns of MMD risk genes derived from single-cell RNA sequencing data of human and mouse brain tissue. Results Of the 24 patients in the discovery cohort, 14 (58.3%) were men and 18 (75.0%) were of European ancestry. Three of 24 discovery cohort probands contained 2 do novo (1-tailed Poisson P = 1.1 × 10-6) and 1 rare, transmitted damaging variant (12.5% of cases) in DIAPH1 (mammalian diaphanous-1), a key regulator of actin remodeling in vascular cells and platelets. Four additional ultrarare damaging heterozygous DIAPH1 variants (3 unphased) were identified in 3 other patients in an 84-proband validation cohort (73.8% female, 77.4% European). All 6 patients were non-East Asian. Compound heterozygous variants were identified in ena/vasodilator-stimulated phosphoproteinlike protein EVL, a mammalian diaphanous-1 interactor that regulates actin polymerization. DIAPH1 and EVL mutant probands had severe, bilateral MMD associated with transfusion-dependent thrombocytopenia. DIAPH1 and other MMD risk genes are enriched in mural cells of midgestational human brain. The DIAPH1 coexpression network converges in vascular cell actin cytoskeleton regulatory pathways. Conclusions and Relevance These findings provide the largest collection to date of non-East Asian individuals with sporadic MMD harboring pathogenic variants in the same gene. The results suggest that DIAPH1 is a novel MMD risk gene and impaired vascular cell actin remodeling in MMD pathogenesis, with diagnostic and therapeutic ramifications.
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Affiliation(s)
- Adam J. Kundishora
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston
| | - Samuel T. Peters
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson
| | - Amélie Pinard
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston
| | - Daniel Duran
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson
| | | | - Tanyeri Barak
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, Connecticut
| | - Danielle F. Miyagishima
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, Connecticut
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Hannah Smith
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston
| | - Jack Ocken
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston
| | - Ashley Dunbar
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | | | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, United Kingdom
| | - Rebecca L. Walker
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Dean Thumkeo
- Department of Drug Discovery Medicine, Kyoto University, Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Arnaud Marlier
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Phan Q. Duy
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston
| | - Nicholas S. Diab
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Benjamin C. Reeves
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston
| | | | | | - Amber N. Stratman
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri
| | - Yi-Hsien Chen
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Shujuan Zhao
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Isabelle Roszko
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Shrikant Mane
- Yale Center for Genome Analysis, West Haven, Connecticut
| | | | | | | | | | | | - Daniel H. Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles
| | - Shih-Shan Lang Chen
- Division of Neurosurgery, Children's Hospital of Philadelphia, Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Phillip B. Storm
- Division of Neurosurgery, Children's Hospital of Philadelphia, Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Michael L. Diluna
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Charles C. Matouk
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Darren B. Orbach
- Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Seth L. Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Edward R. Smith
- Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Richard P. Lifton
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Dianna M. Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Kristopher T. Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, Connecticut
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37
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Srivatsan S, Heidl S, Pfau B, Martin BK, Han PD, Zhong W, van Raay K, McDermot E, Opsahl J, Gamboa L, Smith N, Truong M, Cho S, Barrow KA, Rich LM, Stone J, Wolf CR, McCulloch DJ, Kim AE, Brandstetter E, Sohlberg SL, Ilcisin M, Geyer RE, Chen W, Gehring J, Kosuri S, Bedford T, Rieder MJ, Nickerson DA, Chu HY, Konnick EQ, Debley JS, Shendure J, Lockwood CM, Starita LM. SwabExpress: An end-to-end protocol for extraction-free covid-19 testing. Clin Chem 2021; 68:143-152. [PMID: 34286830 DOI: 10.1093/clinchem/hvab132] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
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Affiliation(s)
- Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sarah Heidl
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Brian Pfau
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Peter D Han
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Weizhi Zhong
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | | | - Evan McDermot
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Jordan Opsahl
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Luis Gamboa
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Nahum Smith
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Melissa Truong
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Shari Cho
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Kaitlyn A Barrow
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jeremy Stone
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Denise J McCulloch
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Ashley E Kim
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | | | - Sarah L Sohlberg
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rachel E Geyer
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jase Gehring
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Sriram Kosuri
- Octant, Inc. Emeryville CA, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Trevor Bedford
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Helen Y Chu
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Eric Q Konnick
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute. Seattle, WA, USA
| | - Christina M Lockwood
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
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38
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Huyghe JR, Harrison TA, Bien SA, Hampel H, Figueiredo JC, Schmit SL, Conti DV, Chen S, Qu C, Lin Y, Barfield R, Baron JA, Cross AJ, Diergaarde B, Duggan D, Harlid S, Imaz L, Kang HM, Levine DM, Perduca V, Perez-Cornago A, Sakoda LC, Schumacher FR, Slattery ML, Toland AE, van Duijnhoven FJB, Van Guelpen B, Agudo A, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Banbury BL, Bassik MC, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Boutron-Ruault MC, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Caan BJ, Campbell PT, Carr PR, Castells A, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Curtis KR, de la Chapelle A, Easton DF, English DR, Feskens EJM, Gala M, Gallinger SJ, Gauderman WJ, Giles GG, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Jenab M, Jenkins MA, Joshi AD, Keku TO, Kooperberg C, Kühn T, Küry S, Le Marchand L, Lejbkowicz F, Li CI, Li L, Lieb W, Lindblom A, Lindor NM, Männistö S, Markowitz SD, Milne RL, Moreno L, Murphy N, Nassir R, Offit K, Ogino S, Panico S, Parfrey PS, Pearlman R, Pharoah PDP, Phipps AI, Platz EA, Potter JD, Prentice RL, Qi L, Raskin L, Rennert G, Rennert HS, Riboli E, Schafmayer C, Schoen RE, Seminara D, Song M, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Trichopoulou A, Ulrich CM, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abecasis GR, Nickerson DA, Scacheri PC, Kundaje A, Casey G, Gruber SB, Hsu L, Moreno V, Hayes RB, Newcomb PA, Peters U. Genetic architectures of proximal and distal colorectal cancer are partly distinct. Gut 2021; 70:1325-1334. [PMID: 33632709 PMCID: PMC8223655 DOI: 10.1136/gutjnl-2020-321534] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/26/2020] [Accepted: 12/18/2020] [Indexed: 01/14/2023]
Abstract
OBJECTIVE An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined. DESIGN To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling. RESULTS We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer. CONCLUSION Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.
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Affiliation(s)
- Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | - David V Conti
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Sai Chen
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Yi Lin
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Richard Barfield
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John A Baron
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Amanda J Cross
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - David Duggan
- Translational Genomics Research Institute - An Affiliate of City of Hope, Phoenix, Arizona, USA
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Liher Imaz
- Public Health Division of Gipuzkoa, Health Department of Basque Country, San Sebastian, Spain
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - David M Levine
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Vittorio Perduca
- Laboratoire de Mathématiques Appliquées MAP5 (UMR CNRS 8145), Université Paris Descartes, Paris, France
- Centre for Research in Epidemiology and Population Health (CESP), Institut pour la Santé et la Recherche Médicale (INSERM) U1018, Université Paris-Saclay, Villejuif, France
| | - Aurora Perez-Cornago
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lori C Sakoda
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Antonio Agudo
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - M Henar Alonso
- Cancer Prevention and Control Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Kristin Anderson
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Barbara L Banbury
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Juergen Boehm
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah Health, Salt Lake City, Utah, USA
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Marie-Christine Boutron-Ruault
- Centre for Research in Epidemiology and Population Health (CESP), Institut pour la Santé et la Recherche Médicale (INSERM) U1018, Université Paris-Saclay, Villejuif, France
- Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Centre (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, California, USA
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia, USA
| | - Prudence R Carr
- Division of Clinical Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Keith R Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dallas R English
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Steven J Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - W James Gauderman
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - John S Grove
- University of Hawai'i Cancer Center, Honolulu, Hawaii, USA
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Robert W Haile
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology, School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Wan-Ling Hsu
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Mazda Jenab
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | | | - Flavio Lejbkowicz
- The Clalit Health Services, Personalized Genomic Service, Carmel Medical Center, Haifa, Israel
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
| | - Christopher I Li
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, PopGen Biobank, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic, Scottsdale, Arizona, USA
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Sanford D Markowitz
- Departments of Medicine and Genetics, Case Comprehensive Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Lorena Moreno
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Neil Murphy
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura'a University, Mecca, Saudi Arabia
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Shuji Ogino
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, University of Naples Federico II, Naples, Italy
| | - Patrick S Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lihong Qi
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, California, USA
| | - Leon Raskin
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel
- Clalit National Cancer Control Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland, USA
| | - Mingyang Song
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Yu-Ru Su
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephen N Thibodeau
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, MayoClinic, Rochester, Minnesota, USA
| | - Duncan C Thomas
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah Health, Salt Lake City, Utah, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O Woods
- Discipline of Genetics, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Anna H Wu
- Department of Preventive Medicine and USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, Ohio, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, California, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California, USA
- City of Hope National Medical Center, Duarte, California, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York, USA
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
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Fohner AE, Dalton R, Skagen K, Jackson K, Claw KG, Hopkins SE, Robinson R, Khan BA, Prasad B, Schuetz EG, Nickerson DA, Thornton TA, Dillard DA, Boyer BB, Thummel KE, Woodahl EL. Characterization of CYP3A pharmacogenetic variation in American Indian and Alaska Native communities, targeting CYP3A4*1G allele function. Clin Transl Sci 2021; 14:1292-1302. [PMID: 33503331 PMCID: PMC8301563 DOI: 10.1111/cts.12970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
The frequencies of genetic variants in the CYP3A4 and CYP3A5 genes differ greatly across global populations, leading to profound differences in the metabolic activity of these enzymes and resulting drug metabolism rates, with important consequences for therapeutic safety and efficacy. Yet, the impact of genetic variants on enzyme activity are incompletely described, particularly in American Indian and Alaska Native (AIAN) populations. To characterize genetic variation in CYP3A4 and CYP3A5 and its effect on enzyme activity, we partnered with AIAN people living in two regions of Alaska: Yup'ik Alaska Native people living in the Yukon-Kuskokwim Delta region of rural southwest Alaska and AIAN people receiving care at the Southcentral Foundation in Anchorage, Alaska. We identified low frequencies of novel and known variation in CYP3A4 and CYP3A5, including low frequencies of the CYP3A4*1G and CYP3A5*1 variants, and linkage disequilibrium patterns that differed from those we previously identified in an American Indian population in western Montana. We also identified increased activity of the CYP3A4*1G allele in vitro and in vivo. We demonstrated that the CYP3A4*1G allele confers increased protein content in human lymphoblastoid cells and both increased protein content and increased activity in human liver microsomes. We confirmed enhanced CYP3A4-mediated 4β-vitamin D hydroxylation activity in Yup'ik people with the CYP3A4*1G allele. AIAN people in Alaska and Montana who carry the CYP3A4*1G allele-coupled with low frequency of the functional CYP3A5*1 variant-may metabolize CYP3A substrates more rapidly than people with the reference CYP3A4 allele.
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Affiliation(s)
- Alison E. Fohner
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Rachel Dalton
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Kasse Skagen
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Konner Jackson
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Katrina G. Claw
- Division of Biomedical Informatics and Personalized MedicineUniversity of ColoradoAuroraColoradoUSA
| | - Scarlett E. Hopkins
- Department of Obstetrics and GynecologyOregon Health & Science UniversityPortlandOregonUSA
| | | | | | - Bhagwat Prasad
- Department of PharmaceuticsUniversity of WashingtonSeattleWashingtonUSA
| | - Erin G. Schuetz
- Department of Pharmaceutical SciencesSt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | | | | | | | - Bert B. Boyer
- Department of Obstetrics and GynecologyOregon Health & Science UniversityPortlandOregonUSA
| | | | - Erica L. Woodahl
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
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Alsharhan H, Ng BG, Daniel EJP, Friedman J, Pivnick EK, Al-Hashem A, Faqeih EA, Liu P, Engelhardt NM, Keller KN, Chen J, Mazzeo PA, Rosenfeld JA, Bamshad MJ, Nickerson DA, Raymond KM, Freeze HH, He M, Edmondson AC, Lam C. Expanding the phenotype, genotype and biochemical knowledge of ALG3-CDG. J Inherit Metab Dis 2021; 44:987-1000. [PMID: 33583022 PMCID: PMC8282734 DOI: 10.1002/jimd.12367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/15/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022]
Abstract
Congenital disorders of glycosylation (CDGs) are a continuously expanding group of monogenic disorders of glycoprotein and glycolipid biosynthesis that cause multisystem diseases. Individuals with ALG3-CDG frequently exhibit severe neurological involvement (epilepsy, microcephaly, and hypotonia), ocular anomalies, dysmorphic features, skeletal anomalies, and feeding difficulties. We present 10 unreported individuals diagnosed with ALG3-CDG based on molecular and biochemical testing with 11 novel variants in ALG3, bringing the total to 40 reported individuals. In addition to the typical multisystem disease seen in ALG3-CDG, we expand the symptomatology of ALG3-CDG to now include endocrine abnormalities, neural tube defects, mild aortic root dilatation, immunodeficiency, and renal anomalies. N-glycan analyses of these individuals showed combined deficiencies of hybrid glycans and glycan extension beyond Man5 GlcNAc2 consistent with their truncated lipid-linked precursor oligosaccharides. This spectrum of N-glycan changes is unique to ALG3-CDG. These expanded features of ALG3-CDG facilitate diagnosis and suggest that optimal management should include baseline endocrine, renal, cardiac, and immunological evaluation at the time of diagnosis and with ongoing monitoring.
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Affiliation(s)
- Hind Alsharhan
- Department of Pediatrics, Division of Human Genetics,
Section of Metabolism, The Children’s Hospital of Philadelphia, Philadelphia,
Pennsylvania
- Department of Pathology and Laboratory Medicine,
Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Faculty of Medicine, Kuwait
University, Kuwait City, Kuwait
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys Medical
Discovery Institute, La Jolla, California
| | - Earnest James Paul Daniel
- Department of Pathology and Laboratory Medicine,
Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jennifer Friedman
- Division of Neurosciences and Pediatrics, University of
California San Diego and Rady Children’s Hospital, San Diego,
California
| | - Eniko K. Pivnick
- Department of Pediatrics, Division of Medical Genetics,
University of Tennessee Health Science Center (UTHSC), Memphis, Tennessee
| | - Amal Al-Hashem
- Department of Pediatrics, Prince Sultan Military Medical
City, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi
Arabia
| | - Eissa Ali Faqeih
- Section of Medical Genetics, Children’s Specialist
Hospital King Fahad Medical City, Riyadh, Saudi Arabia
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor
College of Medicine, Houston, Texas
- Baylor Genetics Laboratories, Houston, Texas
| | - Nicole M. Engelhardt
- Department of Pediatrics, Division of Human Genetics,
Section of Metabolism, The Children’s Hospital of Philadelphia, Philadelphia,
Pennsylvania
| | - Kierstin N. Keller
- Department of Pediatrics, Division of Human Genetics,
Section of Metabolism, The Children’s Hospital of Philadelphia, Philadelphia,
Pennsylvania
| | - Jie Chen
- Department of Pathology and Laboratory Medicine,
Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pamela A. Mazzeo
- Department of Pediatrics, The Children’s Hospital
of Philadelphia, Philadelphia, Pennsylvania
| | | | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor
College of Medicine, Houston, Texas
- Baylor Genetics Laboratories, Houston, Texas
| | - Michael J. Bamshad
- Division of Genetic Medicine, Department of Pediatrics,
University of Washington School of Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington,
Seattle, Washington
- Brotman-Baty Institute, Seattle, Washington
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington,
Seattle, Washington
- Brotman-Baty Institute, Seattle, Washington
| | - Kimiyo M. Raymond
- Department of Laboratory Medicine and Pathology, Mayo
Clinic, Rochester, Minnesota
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical
Discovery Institute, La Jolla, California
| | - Miao He
- Department of Pathology and Laboratory Medicine,
Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew C. Edmondson
- Department of Pediatrics, Division of Human Genetics,
Section of Metabolism, The Children’s Hospital of Philadelphia, Philadelphia,
Pennsylvania
| | - Christina Lam
- Division of Genetic Medicine, Department of Pediatrics,
University of Washington School of Medicine, Seattle, Washington
- Center of Integrated Brain Research, Seattle
Children’s Research Institute, Seattle, Washington
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Acharya A, Raza SI, Anwar MZ, Bharadwaj T, Liaqat K, Khokhar MAS, Everard JL, Nasir A, Nickerson DA, Bamshad MJ, Ansar M, Schrauwen I, Ahmad W, Leal SM. Correction: Wolfram-like syndrome with bicuspid aortic valve due to a homozygous missense variant in CDK13. J Hum Genet 2021; 66:1019. [PMID: 34135457 PMCID: PMC8472884 DOI: 10.1038/s10038-021-00949-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Syed Irfan Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Department of Biochemistry, HBS Medical and Dental College, Islamabad, Pakistan
| | | | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Khurram Liaqat
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Jenna L Everard
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | | | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA. .,Taub Institute for Alzheimer's Disease and The Aging Brain, Columbia University Medical Center, New York, NY, USA.
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Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Ilcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Sci Transl Med 2021; 13:eabf0202. [PMID: 33941621 PMCID: PMC8158963 DOI: 10.1126/scitranslmed.abf0202] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/23/2021] [Accepted: 04/25/2021] [Indexed: 12/16/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gravely affected societies around the world. Outbreaks in different parts of the globe have been shaped by repeated introductions of new viral lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State (USA) to characterize how the spread of SARS-CoV-2 in Washington State in early 2020 was shaped by differences in timing of mitigation strategies across counties and by repeated introductions of viral lineages into the state. In addition, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G but not the other variant (614D) into the state. At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant affects clinical severity or patient outcomes. Overall, this suggests that with regard to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.
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Affiliation(s)
- Nicola F Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Chris D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Louise H Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Benjamin Pelle
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew Richardson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Victoria M Rachleff
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Elisabeth Brandstetter
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Peter D Han
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kirsten Lacombe
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Caitlin R Wolf
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | | | - Barry R Lutz
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Matthew Thompson
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey S Duchin
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Public Health - Seattle & King County, Seattle, WA98121, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Helen Y Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Scott Lindquist
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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Sofer T, Kurniansyah N, Aguet F, Ardlie K, Durda P, Nickerson DA, Smith JD, Liu Y, Gharib SA, Redline S, Rich SS, Rotter JI, Taylor KD. Benchmarking association analyses of continuous exposures with RNA-seq in observational studies. Brief Bioinform 2021; 22:6278609. [PMID: 34015820 DOI: 10.1093/bib/bbab194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/12/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
Large datasets of hundreds to thousands of individuals measuring RNA-seq in observational studies are becoming available. Many popular software packages for analysis of RNA-seq data were constructed to study differences in expression signatures in an experimental design with well-defined conditions (exposures). In contrast, observational studies may have varying levels of confounding transcript-exposure associations; further, exposure measures may vary from discrete (exposed, yes/no) to continuous (levels of exposure), with non-normal distributions of exposure. We compare popular software for gene expression-DESeq2, edgeR and limma-as well as linear regression-based analyses for studying the association of continuous exposures with RNA-seq. We developed a computation pipeline that includes transformation, filtering and generation of empirical null distribution of association P-values, and we apply the pipeline to compute empirical P-values with multiple testing correction. We employ a resampling approach that allows for assessment of false positive detection across methods, power comparison and the computation of quantile empirical P-values. The results suggest that linear regression methods are substantially faster with better control of false detections than other methods, even with the resampling method to compute empirical P-values. We provide the proposed pipeline with fast algorithms in an R package Olivia, and implemented it to study the associations of measures of sleep disordered breathing with RNA-seq in peripheral blood mononuclear cells in participants from the Multi-Ethnic Study of Atherosclerosis.
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Affiliation(s)
- Tamar Sofer
- Program of Sleep Medicine Epidemiology at the Brigham and Women's Hospital, USA
| | - Nuzulul Kurniansyah
- Program of Sleep Medicine Epidemiology at the Brigham and Women's Hospital, USA
| | | | | | - Peter Durda
- Department of Pathology & Laboratory Medicine at the University of Vermont, USA
| | - Deborah A Nickerson
- Genome Sciences and the Principal Investigator of the Human Genetics and Translational Genomics program at the University of Washington, USA
| | - Joshua D Smith
- Human Genetics and Translational Genomics program at the University of Washington, USA
| | | | - Sina A Gharib
- Computational Medicine Core at the Center of Lung Biology at the University of Washington, USA
| | - Susan Redline
- Harvard School of Medicine and the director of the program in Sleep Medicine Epidemiology at Brigham and Women's Hospital, USA
| | - Stephen S Rich
- Center for Public Health Genomics at the University of Virginia, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences at the Harbor-UCLA Medical Center at the Lundquist Institute, USA
| | - Kent D Taylor
- Harbor-UCLA Medical Center at the Lundquist Institute, USA
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Srivatsan S, Heidl S, Pfau B, Martin BK, Han PD, Zhong W, van Raay K, McDermot E, Opsahl J, Gamboa L, Smith N, Truong M, Cho S, Barrow KA, Rich LM, Stone J, Wolf CR, McCulloch DJ, Kim AE, Brandstetter E, Sohlberg SL, Ilcisin M, Geyer RE, Chen W, Gehring J, Kosuri S, Bedford T, Rieder MJ, Nickerson DA, Chu HY, Konnick EQ, Debley JS, Shendure J, Lockwood CM, Starita LM. SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing. bioRxiv 2021:2020.04.22.056283. [PMID: 32511368 PMCID: PMC7263496 DOI: 10.1101/2020.04.22.056283] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral activation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
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Affiliation(s)
- Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Sarah Heidl
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Brian Pfau
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Peter D. Han
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Weizhi Zhong
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | | | - Evan McDermot
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Jordan Opsahl
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Luis Gamboa
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Nahum Smith
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Melissa Truong
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Shari Cho
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Kaitlyn A. Barrow
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Jeremy Stone
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Caitlin R. Wolf
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Denise J. McCulloch
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Ashley E. Kim
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | | | - Sarah L. Sohlberg
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rachel E. Geyer
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Jase Gehring
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | | | - Sriram Kosuri
- Octant, Inc. Emeryville CA, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles CA, USA
| | - Trevor Bedford
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark J. Rieder
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Helen Y. Chu
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Eric Q. Konnick
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Laboratory Medicine and Pathology, Seattle WA, USA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Howard Hughes Medical Institute. Seattle WA, USA
| | - Christina M. Lockwood
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Laboratory Medicine and Pathology, Seattle WA, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Acharya A, Raza SI, Anwar MZ, Bharadwaj T, Liaqat K, Khokhar MAS, Everard JL, Nasir A, Nickerson DA, Bamshad MJ, Ansar M, Schrauwen I, Ahmad W, Leal SM. Wolfram-like syndrome with bicuspid aortic valve due to a homozygous missense variant in CDK13. J Hum Genet 2021; 66:1009-1018. [PMID: 33879837 PMCID: PMC8472924 DOI: 10.1038/s10038-021-00922-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/03/2022]
Abstract
Background Wolfram syndrome (WFS) is characterized by deafness, diabetes mellitus, and diabetes insipidus along with optic atrophy. WFS has an autosomal recessive mode of inheritance and is due to variants in WFS1 and CISD2. Methods We evaluated the underlying molecular etiology of three affected members of a consanguineous family with hearing impairment, bicuspid aortic valve, diabetes mellitus and insipidus, clinodactyly, and gastrointestinal tract abnormalities via exome sequencing approach. We correlated clinical and imaging data with the genetic findings and their associated phenotypes. Results We identified a homozygous missense variant p.(Asn1097Lys) in CDK13, a gene previously associated with autosomal dominant congenital heart defects, dysmorphic facial features, clinodactyly, gastrointestinal tract abnormalities, intellectual developmental disorder, and seizures with variable phenotypic features. Conclusion We report a homozygous variant in CDK13 and suggest that this gene causes an autosomal recessive disorder with hearing impairment, bicuspid aortic valve, diabetes mellitus and insipidus, clinodactyly, and gastrointestinal tract abnormalities.
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Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Syed Irfan Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Department of Biochemistry, HBS Medical and Dental College, Islamabad, Pakistan
| | | | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Khurram Liaqat
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Jenna L Everard
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | | | | | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA. .,Taub Institute for Alzheimer's Disease and The Aging Brain, Columbia University Medical Center, New York, NY, USA.
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Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA, Shen Y, Lettice LA, Silveira-Lucas EL, Petit F, Ahituv N. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nat Commun 2021; 12:2282. [PMID: 33863876 PMCID: PMC8052326 DOI: 10.1038/s41467-021-22470-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/12/2021] [Indexed: 12/18/2022] Open
Abstract
Acheiropodia, congenital limb truncation, is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development. How these deletions lead to this phenotype is unknown. Using whole-genome sequencing, we fine-mapped the acheiropodia-associated region to 12 kb and show that it does not function as an enhancer. CTCF and RAD21 ChIP-seq together with 4C-seq and DNA FISH identify three CTCF sites within the acheiropodia-deleted region that mediate the interaction between the ZRS and the SHH promoter. This interaction is substituted with other CTCF sites centromeric to the ZRS in the disease state. Mouse knockouts of the orthologous 12 kb sequence have no apparent abnormalities, showcasing the challenges in modelling CTCF alterations in animal models due to inherent motif differences between species. Our results show that alterations in CTCF motifs can lead to a Mendelian condition due to altered enhancer-promoter interactions.
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Affiliation(s)
- Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Chenling Xiong
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Lauren Kane
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Kirsty Jamieson
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute, Seattle, WA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Laura A Lettice
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Florence Petit
- CHU Lille, University of Lille, EA7364 RADEME, Lille, France
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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47
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Natarajan P, Pampana A, Graham SE, Ruotsalainen SE, Perry JA, de Vries PS, Broome JG, Pirruccello JP, Honigberg MC, Aragam K, Wolford B, Brody JA, Antonacci-Fulton L, Arden M, Aslibekyan S, Assimes TL, Ballantyne CM, Bielak LF, Bis JC, Cade BE, Do R, Doddapaneni H, Emery LS, Hung YJ, Irvin MR, Khan AT, Lange L, Lee J, Lemaitre RN, Martin LW, Metcalf G, Montasser ME, Moon JY, Muzny D, O'Connell JR, Palmer ND, Peralta JM, Peyser PA, Stilp AM, Tsai M, Wang FF, Weeks DE, Yanek LR, Wilson JG, Abecasis G, Arnett DK, Becker LC, Blangero J, Boerwinkle E, Bowden DW, Chang YC, Chen YDI, Choi WJ, Correa A, Curran JE, Daly MJ, Dutcher SK, Ellinor PT, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, He J, Hveem K, Jarvik GP, Kaplan RC, Kardia SLR, Kenny E, Kim RW, Kooperberg C, Laurie CC, Lee S, Lloyd-Jones DM, Loos RJF, Lubitz SA, Mathias RA, Martinez KAV, McGarvey ST, Mitchell BD, Nickerson DA, North KE, Palotie A, Park CJ, Psaty BM, Rao DC, Redline S, Reiner AP, Seo D, Seo JS, Smith AV, Tracy RP, Vasan RS, Kathiresan S, Cupples LA, Rotter JI, Morrison AC, Rich SS, Ripatti S, Willer C, Peloso GM. Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices. Nat Commun 2021; 12:2182. [PMID: 33846329 PMCID: PMC8042019 DOI: 10.1038/s41467-021-22339-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
Autosomal genetic analyses of blood lipids have yielded key insights for coronary heart disease (CHD). However, X chromosome genetic variation is understudied for blood lipids in large sample sizes. We now analyze genetic and blood lipid data in a high-coverage whole X chromosome sequencing study of 65,322 multi-ancestry participants and perform replication among 456,893 European participants. Common alleles on chromosome Xq23 are strongly associated with reduced total cholesterol, LDL cholesterol, and triglycerides (min P = 8.5 × 10-72), with similar effects for males and females. Chromosome Xq23 lipid-lowering alleles are associated with reduced odds for CHD among 42,545 cases and 591,247 controls (P = 1.7 × 10-4), and reduced odds for diabetes mellitus type 2 among 54,095 cases and 573,885 controls (P = 1.4 × 10-5). Although we observe an association with increased BMI, waist-to-hip ratio adjusted for BMI is reduced, bioimpedance analyses indicate increased gluteofemoral fat, and abdominal MRI analyses indicate reduced visceral adiposity. Co-localization analyses strongly correlate increased CHRDL1 gene expression, particularly in adipose tissue, with reduced concentrations of blood lipids.
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Affiliation(s)
- Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Akhil Pampana
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Sarah E Graham
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Sanni E Ruotsalainen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - James A Perry
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - James P Pirruccello
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael C Honigberg
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Krishna Aragam
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Brooke Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lucinda Antonacci-Fulton
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Moscati Arden
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Christie M Ballantyne
- Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX, USA
- Houston Methodist Debakey Heart and Vascular Center, Houston, TX, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital Songshan branch, Taipei, Taiwan
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alyna T Khan
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jiwon Lee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lisa W Martin
- Division of Cardiology, George Washington University School of Medicine and Healthcare Sciences, Washington, DC, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - May E Montasser
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey R O'Connell
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Michael Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Fei Fei Wang
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Daniel E Weeks
- Departments of Human Genetics and Biostatistics, University of Pittsburgh, Pittsburgh, Pittsburgh, PA, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Donna K Arnett
- Deans office, School of Public Health, University of Kentucky, Lexington, KY, USA
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yi-Cheng Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yii-Der I Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Won Jung Choi
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Susan K Dutcher
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital, Boston, MA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-, Salem, NC, USA
| | - Stacey Gabriel
- Genomics Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, and Tulane University Translational Science Institute, Tulane University, New Orleans, LA, USA
| | - Kristian Hveem
- Department of Public Health and General Practice, HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Dept of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Eimear Kenny
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan W Kim
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Seonwook Lee
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Don M Lloyd-Jones
- Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven A Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital, Boston, MA, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Stephen T McGarvey
- Department of Epidemiology and International Health Institute, Brown University, Providence, RI, USA
| | - Braxton D Mitchell
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- University of Washington Center for Mendelian Genomics, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aarno Palotie
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cheol Joo Park
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Departments of Epidemiology and Health Services, University of Washington, Seattle, WA, USA
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daekwan Seo
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Jeong-Sun Seo
- Psomagen. Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- The Icelandic Heart Association, Kopavogur, Iceland
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larrner College of Medicine, University of Vermont, Colchester, VT, USA
| | - Ramachandran S Vasan
- Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Verve Therapeutics, Cambridge, MA, USA
| | - L Adrienne Cupples
- NHLBI Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Samuli Ripatti
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Cristen Willer
- Department of Internal Medicine: Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
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48
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Jackson ML, Hart GR, McCulloch DJ, Adler A, Brandstetter E, Fay K, Han P, Lacombe K, Lee J, Sibley TR, Nickerson DA, Rieder MJ, Starita L, Englund JA, Bedford T, Chu H, Famulare M. Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study. BMC Infect Dis 2021; 21:335. [PMID: 33836685 PMCID: PMC8033554 DOI: 10.1186/s12879-021-06028-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/31/2021] [Indexed: 02/13/2023] Open
Abstract
Background Unusually high snowfall in western Washington State in February 2019 led to widespread school and workplace closures. We assessed the impact of social distancing caused by this extreme weather event on the transmission of respiratory viruses. Methods Residual specimens from patients evaluated for acute respiratory illness at hospitals in the Seattle metropolitan area were screened for a panel of respiratory viruses. Transmission models were fit to each virus to estimate the magnitude reduction in transmission due to weather-related disruptions. Changes in contact rates and care-seeking were informed by data on local traffic volumes and hospital visits. Results Disruption in contact patterns reduced effective contact rates during the intervention period by 16 to 95%, and cumulative disease incidence through the remainder of the season by 3 to 9%. Incidence reductions were greatest for viruses that were peaking when the disruption occurred and least for viruses in an early epidemic phase. Conclusion High-intensity, short-duration social distancing measures may substantially reduce total incidence in a respiratory virus epidemic if implemented near the epidemic peak. For SARS-CoV-2, this suggests that, even when SARS-CoV-2 spread is out of control, implementing short-term disruptions can prevent COVID-19 deaths. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06028-4.
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Affiliation(s)
- Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA.
| | | | - Denise J McCulloch
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter Han
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Lea Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Helen Chu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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49
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Hildebrandt CC, Patel N, Graham JM, Bamshad M, Nickerson DA, White JJ, Marvin CT, Miller DE, Grand KL, Sanchez-Lara PA, Schweitzer D, Al-Zaidan HI, Al Masseri Z, Alkuraya FS, Lin AE. Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome. Am J Med Genet A 2021; 185:2136-2149. [PMID: 33783941 DOI: 10.1002/ajmg.a.62194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/18/2021] [Accepted: 02/27/2021] [Indexed: 12/29/2022]
Abstract
Van den Ende-Gupta syndrome (VDEGS) is a rare autosomal recessive condition characterized by distinctive facial and skeletal features, and in most affected persons, by biallelic pathogenic variants in SCARF2. We review the type and frequency of the clinical features in 36 reported individuals with features of VDEGS, 15 (42%) of whom had known pathogenic variants in SCARF2, 6 (16%) with negative SCARF2 testing, and 15 (42%) not tested. We also report three new individuals with pathogenic variants in SCARF2 and clinical features of VDEGS. Of the six persons without known pathogenic variants in SCARF2, three remain unsolved despite extensive genetic testing. Three were found to have pathogenic ABL1 variants using whole exome sequencing (WES) or whole genome sequencing (WGS). Their phenotype was consistent with the congenital heart disease and skeletal malformations syndrome (CHDSKM), which has been associated with ABL1 variants. Of the three unsolved cases, two were brothers who underwent WGS and targeted long-range sequencing of both SCARF2 and ABL1, and the third person who underwent WES and RNA sequencing for SCARF2. Because these affected individuals with classical features of VDEGS lacked a detectable pathogenic SCARF2 variant, genetic heterogeneity is likely. Our study shows the importance of performing genetic testing on individuals with the VDEGS "phenotype," either as a targeted gene analysis (SCARF2, ABL1) or WES/WGS. Additionally, individuals with the combination of arachnodactyly and blepharophimosis should undergo echocardiography while awaiting results of molecular testing due to the overlapping physical features of VDEGS and CHDSKM.
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Affiliation(s)
- Clara C Hildebrandt
- Genetics Unit, MassGeneral Hospital for Children, Massachusetts, USA.,Boston Children's Hospital Medical Biochemical Fellowship, Boston, Massachusetts, USA
| | - Nisha Patel
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - John M Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Michael Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute, Seattle, Washington, USA
| | | | - Colby T Marvin
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Katheryn L Grand
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Daniela Schweitzer
- Division of Pediatric Genetics, Department of Pediatrics, University of California Los Angeles, Los Angeles, California, USA
| | - Hamad I Al-Zaidan
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Zainab Al Masseri
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Angela E Lin
- Genetics Unit, MassGeneral Hospital for Children, Massachusetts, USA
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50
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Allenspach EJ, Soveg F, Finn LS, So L, Gorman JA, Rosen ABI, Skoda-Smith S, Wheeler MM, Barrow KA, Rich LM, Debley JS, Bamshad MJ, Nickerson DA, Savan R, Torgerson TR, Rawlings DJ. Germline SAMD9L truncation variants trigger global translational repression. J Exp Med 2021; 218:211891. [PMID: 33724365 PMCID: PMC7970252 DOI: 10.1084/jem.20201195] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/07/2021] [Accepted: 02/12/2021] [Indexed: 12/11/2022] Open
Abstract
SAMD9L is an interferon-induced tumor suppressor implicated in a spectrum of multisystem disorders, including risk for myeloid malignancies and immune deficiency. We identified a heterozygous de novo frameshift variant in SAMD9L in an infant with B cell aplasia and clinical autoinflammatory features who died from respiratory failure with chronic rhinovirus infection. Autopsy demonstrated absent bone marrow and peripheral B cells as well as selective loss of Langerhans and Purkinje cells. The frameshift variant led to expression of a truncated protein with interferon treatment. This protein exhibited a gain-of-function phenotype, resulting in interference in global protein synthesis via inhibition of translational elongation. Using a mutational scan, we identified a region within SAMD9L where stop-gain variants trigger a similar translational arrest. SAMD9L variants that globally suppress translation had no effect or increased mRNA transcription. The complex-reported phenotype likely reflects lineage-dominant sensitivities to this translation block. Taken together, our findings indicate that interferon-triggered SAMD9L gain-of-function variants globally suppress translation.
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Affiliation(s)
- Eric J Allenspach
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Frank Soveg
- Department of Immunology, University of Washington, Seattle, WA
| | - Laura S Finn
- Department of Pathology and Laboratory Medicine, University of Washington, Seattle, WA
| | - Lomon So
- Department of Immunology, University of Washington, Seattle, WA.,Division of Immunology, Benaroya Research Institute, Seattle, WA
| | - Jacquelyn A Gorman
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | - Aaron B I Rosen
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | | | | | - Kaitlyn A Barrow
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA.,Genome Sciences, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Deborah A Nickerson
- Genome Sciences, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA
| | | | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA.,Department of Immunology, University of Washington, Seattle, WA
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