1
|
Lupski J, Dardas Z, Marafi D, Duan R, Fatih J, El-Rashidy O, Grochowski C, Carvalho C, Jhangiani S, Bi W, Du H, Gibbs R, Posey J, Calame D, Zaki M. Genomic Balancing Act: Deciphering DNA rearrangements in the Complex Chromosomal Aberration involving 5p15.2, 2q31.1 and 18q21.32. Res Sq 2024:rs.3.rs-3949622. [PMID: 38464263 PMCID: PMC10925411 DOI: 10.21203/rs.3.rs-3949622/v1] [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] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Despite extensive research into the genetic underpinnings of neurodevelopmental disorders (NDD), many clinical cases remain unresolved. We studied a female proband with a NDD, mildly dysmorphic facial features, and brain stem hypoplasia on neuroimaging. Comprehensive genomic analyses revealed a terminal 5p loss and terminal 18q gain in the proband while a diploid copy number for chromosomes 5 and 18 in both parents. Genomic investigations in the proband identified an unbalanced translocation t(5;18) with additional genetic material from chromosome 2 (2q31.3) inserted at the breakpoint, pointing to a complex chromosomal rearrangement (CCR) involving 5p15.2, 2q31.3, and 18q21.32. Breakpoint junction analyses enabled by long read genome sequencing unveiled the presence of four distinct junctions in the father, who is carrier of a balanced CCR. The proband inherited from the father both the abnormal chromosome 5 resulting in segmental aneusomies of chr5 (loss) and chr18 (gain) and a der(2) homologue. Evidences suggest a chromoplexy mechanism for this CCR derivation, involving double-strand breaks (DSBs) repaired by non-homologous end joining (NHEJ) or alternative end joining (alt-EJ). The complexity of the CCR and the segregation of homologues elucidate the genetic model for this family. This study demonstrates the importance of combining multiple genomic technologies to uncover genetic causes of complex neurodevelopmental syndrome and to better understand genetic disease mechanisms.
Collapse
|
2
|
Chappell CL, Hoffman KL, Lorenzi PL, Tan L, Petrosino J, Gibbs R, Muzny D, Doddapaneni H, Ross MC, Menon VK, Surathu A, Javornik Cregeen SJ, Reyes AG, Okhuysen PC. Tryptophan Metabolites And Their Predicted Microbial Sources In Fecal Samples From Healthy Individuals. bioRxiv 2024:2023.12.20.572622. [PMID: 38187744 PMCID: PMC10769349 DOI: 10.1101/2023.12.20.572622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Gut microbiota produce tryptophan metabolites (TMs) important to homeostasis. However, measuring TM levels in stool and determining their microbial sources can be difficult. Here, we measured TMs from the indole pathway in fecal samples from 21 healthy adults with the goal to: 1) determine fecal TM concentrations in healthy individuals; 2) link TM levels to bacterial abundance using 16S and whole genome shotgun (WGS) sequencing data; and 3) predict likely bacterial sources of TM production. Within our samples, we identified 151 genera (16S) and 592 bacterial species (WGS). Eight TMs were found in ≥17 fecal samples, including four in all persons. To our knowledge, we are the first to report fecal levels for indole-3-lactate, indole-3-propionate, and 3-indoleacrylate levels in healthy persons. Overall, indole, indole-3-acetate (IAA), and skatole accounted for 86% of the eight TMs measured. Significant correlations were found between seven TMs and 29 bacterial species. Predicted multiple TM sources support the notion of a complex network of TM production and regulation. Further, the data suggest key roles for Collinsella aerofaciens and IAA, a metabolite reported to maintain intestinal homeostasis through enhanced barrier integrity and anti-inflammatory/antioxidant activities. These findings extend our understanding of TMs and their relationship to the microbial species that act as effectors and/or regulators in the healthy intestine and may lead to novel strategies designed to manipulate tryptophan metabolism to prevent disease and/or restore health to the dysbiotic gut.
Collapse
|
3
|
Hong YS, Battle SL, Shi W, Puiu D, Pillalamarri V, Xie J, Pankratz N, Lake NJ, Lek M, Rotter JI, Rich SS, Kooperberg C, Reiner AP, Auer PL, Heard-Costa N, Liu C, Lai M, Murabito JM, Levy D, Grove ML, Alonso A, Gibbs R, Dugan-Perez S, Gondek LP, Guallar E, Arking DE. Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality. Nat Commun 2023; 14:6113. [PMID: 37777527 PMCID: PMC10542802 DOI: 10.1038/s41467-023-41785-7] [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: 05/14/2023] [Accepted: 09/14/2023] [Indexed: 10/02/2023] Open
Abstract
Mitochondria carry their own circular genome and disruption of the mitochondrial genome is associated with various aging-related diseases. Unlike the nuclear genome, mitochondrial DNA (mtDNA) can be present at 1000 s to 10,000 s copies in somatic cells and variants may exist in a state of heteroplasmy, where only a fraction of the DNA molecules harbors a particular variant. We quantify mtDNA heteroplasmy in 194,871 participants in the UK Biobank and find that heteroplasmy is associated with a 1.5-fold increased risk of all-cause mortality. Additionally, we functionally characterize mtDNA single nucleotide variants (SNVs) using a constraint-based score, mitochondrial local constraint score sum (MSS) and find it associated with all-cause mortality, and with the prevalence and incidence of cancer and cancer-related mortality, particularly leukemia. These results indicate that mitochondria may have a functional role in certain cancers, and mitochondrial heteroplasmic SNVs may serve as a prognostic marker for cancer, especially for leukemia.
Collapse
Affiliation(s)
- Yun Soo Hong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie L Battle
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Natural Sciences, College of Arts and Sciences, Bowie State University, Bowie, MD, USA
| | - Wen Shi
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Vamsee Pillalamarri
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiaqi Xie
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, 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
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health & Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nancy Heard-Costa
- Departments of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Meng Lai
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Joanne M Murabito
- Section of General Internal Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Megan L Grove
- 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
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Shannon Dugan-Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Eliseo Guallar
- Department of Epidemiology and Medicine, and Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
4
|
Hanna L, Jha R, Sounderajah V, Markar S, Gibbs R. Patient Reported Outcome Measures Used to Assess Quality of Life in Aortic Dissection: a Systematic Scoping Review using COSMIN Methodology. Eur J Vasc Endovasc Surg 2023; 66:343-350. [PMID: 37391013 DOI: 10.1016/j.ejvs.2023.06.032] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023]
Abstract
OBJECTIVE To systematically identify all patient reported outcome measures (PROMs) (quality of life [QOL] instruments or other instrument/methodology) that have been used to date in aortic dissection (AD) and to explore how well these instruments evaluate QOL according to the Consensus based Standards for the selection of health Measurement Instruments (COSMIN) methodology or guideline. DATA SOURCES Embase, MEDLINE, PsycINFO, CINAHL, and Cochrane Library were search on 1st July 2022. REVIEW METHODS This scoping review was undertaken according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews (PRISMA-ScR) and the COSMIN guidelines for performing systematic reviews of validated PROMs. Studies that reported on any aspect or domain of QOL using a PROM or other instrument or methodology on AD were included. Data synthesis, including psychometric property analysis and risk of bias assessment were performed according to COSMIN guidelines. RESULTS Forty-five studies, published between 1994 and 2021 reporting on 5 874 patients (mean age 63 years, 70.6% male), were included. A total of 39 PROMs were used, and three studies used semi-structured interviews. The majority (69%) of studies were in patients with type A aortic dissection (TAAD). The most common PROM used was the SF-36 (51%). Six studies evaluated one or more psychometric properties of a PROM. Only one of these studies was specifically designed as a validation study. No study reported on content validity. Internal consistency was the most evaluated psychometric property. No study evaluated all the psychometric properties according to COSMIN methodology. The methodological quality used to assess these PROMs was judged to be adequate or very good. CONCLUSION This review highlights the heterogeneity of PROMs or methods used to determine QOL in AD patients. The lack of research regarding a comprehensive evaluation of the psychometric properties of a PROM used in AD highlights the need for the development and validation of a dissection specific PROM. [PROSPERO registration no. CRD42022310477].
Collapse
Affiliation(s)
- Lydia Hanna
- Department of Surgery and Cancer, Imperial College London, London, UK; Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK.
| | - Rama Jha
- School of Medicine, Imperial College London, London, UK
| | - Viknesh Sounderajah
- Department of Surgery and Cancer, Imperial College London, London, UK; Institute of Global Health Innovation, Imperial College London, London, UK
| | - Sheraz Markar
- Department of Surgery and Cancer, Imperial College London, London, UK; Nuffield Department of Surgery, University of Oxford, Oxford, UK
| | - Richard Gibbs
- Department of Surgery and Cancer, Imperial College London, London, UK; Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| |
Collapse
|
5
|
Einson J, Glinos D, Boerwinkle E, Castaldi P, Darbar D, de Andrade M, Ellinor P, Fornage M, Gabriel S, Germer S, Gibbs R, Hersh CP, Johnsen J, Kaplan R, Konkle BA, Kooperberg C, Nassir R, Loos RJF, Meyers DA, Mitchell BD, Psaty B, Vasan RS, Rich SS, Rienstra M, Rotter JI, Saferali A, Shoemaker MB, Silverman E, Smith AV, Mohammadi P, Castel SE, Iossifov I, Lappalainen T. Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. Genetics 2023; 224:iyad115. [PMID: 37348055 PMCID: PMC10411602 DOI: 10.1093/genetics/iyad115] [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: 02/02/2023] [Revised: 02/02/2023] [Accepted: 04/18/2023] [Indexed: 06/24/2023] Open
Abstract
Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-sequencing data in GTEx V8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased whole genome sequencing data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.
Collapse
Affiliation(s)
- Jonah Einson
- Department of Biomedical Informatics, Columbia University, New York, NY 10027, USA
- New York Genome Center, New York, NY 10013, USA
| | | | - Eric Boerwinkle
- School of Public Health, University of Texas Health at Houston, Houston, TX 77030, USA
| | - Peter Castaldi
- Department of Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Dawood Darbar
- Department of Cardiology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mariza de Andrade
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Patrick Ellinor
- Corrigan Minehan Heart Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health at Houston, Houston, TX 77030, USA
| | | | | | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine Human Genome Sequencing Center, Houston, TX 77030, USA
| | - Craig P Hersh
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jill Johnsen
- Department of Hematology, University of Washington, Seattle, WA 98195, USA
| | - Robert Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Barbara A Konkle
- Department of Hematology, University of Washington, Seattle, WA 98195, USA
| | | | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura University, Mecca 24382, Saudi Arabia
| | - Ruth J F Loos
- Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deborah A Meyers
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Braxton D Mitchell
- Department of Medicine, 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
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA 98195, USA
| | | | - Stephen S Rich
- Public Health Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Michael Rienstra
- Clinical Cardiology, UMCG Cardiology, Groningen 09713, the Netherlands
| | - 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
| | - Aabida Saferali
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Edwin Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Albert Vernon Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephane E Castel
- New York Genome Center, New York, NY 10013, USA
- Variant Bio, Seattle, WA 98102, USA
| | - Ivan Iossifov
- New York Genome Center, New York, NY 10013, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10027, USA
- Department of Gene Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| |
Collapse
|
6
|
Olsson KW, Mani K, Burdess A, Patterson S, Scali ST, Kölbel T, Panuccio G, Eleshra A, Bertoglio L, Ardita V, Melissano G, Acharya A, Bicknell C, Riga C, Gibbs R, Jenkins M, Bakthavatsalam A, Sweet MP, Kasprzak PM, Pfister K, Oikonomou K, Heloise T, Sobocinski J, Butt T, Dias N, Tang C, Cheng SWK, Vandenhaute S, Van Herzeele I, Sorber RA, Black JH, Tenorio ER, Oderich GS, Vincent Z, Khashram M, Eagleton MJ, Pedersen SF, Budtz-Lilly J, Lomazzi C, Bissacco D, Trimarchi S, Huerta A, Riambau V, Wanhainen A. Outcomes After Endovascular Aortic Intervention in Patients With Connective Tissue Disease. JAMA Surg 2023; 158:832-839. [PMID: 37314760 PMCID: PMC10267845 DOI: 10.1001/jamasurg.2023.2128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/03/2023] [Indexed: 06/15/2023]
Abstract
IMPORTANCE Endovascular treatment is not recommended for aortic pathologies in patients with connective tissue diseases (CTDs) other than in redo operations and as bridging procedures in emergencies. However, recent developments in endovascular technology may challenge this dogma. OBJECTIVE To assess the midterm outcomes of endovascular aortic repair in patients with CTD. DESIGN, SETTING, AND PARTICIPANTS For this descriptive retrospective study, data on demographics, interventions, and short-term and midterm outcomes were collected from 18 aortic centers in Europe, Asia, North America, and New Zealand. Patients with CTD who had undergone endovascular aortic repair from 2005 to 2020 were included. Data were analyzed from December 2021 to November 2022. EXPOSURE All principal endovascular aortic repairs, including redo surgery and complex repairs of the aortic arch and visceral aorta. MAIN OUTCOMES AND MEASURES Short-term and midterm survival, rates of secondary procedures, and conversion to open repair. RESULTS In total, 171 patients were included: 142 with Marfan syndrome, 17 with Loeys-Dietz syndrome, and 12 with vascular Ehlers-Danlos syndrome (vEDS). Median (IQR) age was 49.9 years (37.9-59.0), and 107 patients (62.6%) were male. One hundred fifty-two (88.9%) were treated for aortic dissections and 19 (11.1%) for degenerative aneurysms. One hundred thirty-six patients (79.5%) had undergone open aortic surgery before the index endovascular repair. In 74 patients (43.3%), arch and/or visceral branches were included in the repair. Primary technical success was achieved in 168 patients (98.2%), and 30-day mortality was 2.9% (5 patients). Survival at 1 and 5 years was 96.2% and 80.6% for Marfan syndrome, 93.8% and 85.2% for Loeys-Dietz syndrome, and 75.0% and 43.8% for vEDS, respectively. After a median (IQR) follow-up of 4.7 years (1.9-9.2), 91 patients (53.2%) had undergone secondary procedures, of which 14 (8.2%) were open conversions. CONCLUSIONS AND RELEVANCE This study found that endovascular aortic interventions, including redo procedures and complex repairs of the aortic arch and visceral aorta, in patients with CTD had a high rate of early technical success, low perioperative mortality, and a midterm survival rate comparable with reports of open aortic surgery in patients with CTD. The rate of secondary procedures was high, but few patients required conversion to open repair. Improvements in devices and techniques, as well as ongoing follow-up, may result in endovascular treatment for patients with CTD being included in guideline recommendations.
Collapse
Affiliation(s)
| | - Kevin Mani
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Anne Burdess
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Suzannah Patterson
- Division of Vascular Surgery and Endovascular Therapy, University of Florida, Gainesville
| | - Salvatore T. Scali
- Division of Vascular Surgery and Endovascular Therapy, University of Florida, Gainesville
| | - Tilo Kölbel
- Department of Vascular Medicine, German Aortic Center, University Heart Center, Hamburg, Germany
| | - Giuseppe Panuccio
- Department of Vascular Medicine, German Aortic Center, University Heart Center, Hamburg, Germany
| | - Ahmed Eleshra
- Department of Vascular Medicine, German Aortic Center, University Heart Center, Hamburg, Germany
| | - Luca Bertoglio
- Division of Vascular Surgery, Vita Salute San Raffaele University, San Raffaele Hospital, Milano, Italy
| | - Vincenzo Ardita
- Division of Vascular Surgery, Vita Salute San Raffaele University, San Raffaele Hospital, Milano, Italy
| | - Germano Melissano
- Division of Vascular Surgery, Vita Salute San Raffaele University, San Raffaele Hospital, Milano, Italy
| | - Amish Acharya
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Colin Bicknell
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Celia Riga
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Richard Gibbs
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Michael Jenkins
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Arvind Bakthavatsalam
- Division of Vascular Surgery, Department of Surgery, University of Washington Medical Center, Seattle
| | - Matthew P. Sweet
- Division of Vascular Surgery, Department of Surgery, University of Washington Medical Center, Seattle
| | - Piotr M. Kasprzak
- Department of Vascular and Endovascular Surgery, University Medical Centre Regensburg, Regensburg, Germany
| | - Karin Pfister
- Department of Vascular and Endovascular Surgery, University Medical Centre Regensburg, Regensburg, Germany
| | - Kyriakos Oikonomou
- Department of Vascular and Endovascular Surgery, University Medical Centre Regensburg, Regensburg, Germany
- Department of Vascular and Endovascular Surgery, Cardiovascular Surgery Clinic, University Hospital Frankfurt and Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Tessely Heloise
- Department of Vascular Surgery, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Jonathan Sobocinski
- Department of Vascular Surgery, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Talha Butt
- Vascular Center, Skåne University Hospital and Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Nuno Dias
- Vascular Center, Skåne University Hospital and Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Ching Tang
- Department of Surgery, Queen Mary Hospital, Hong Kong, China
| | - Stephen W. K. Cheng
- Division of Vascular & Endovascular Surgery, Department of Surgery, University of Hong Kong Medical Centre, Hong Kong, China
| | - Sarah Vandenhaute
- Department of Thoracic and Vascular Surgery, Ghent University Hospital, Ghent, Belgium
| | - Isabelle Van Herzeele
- Department of Thoracic and Vascular Surgery, Ghent University Hospital, Ghent, Belgium
| | - Rebecca A. Sorber
- Department of Vascular Surgery and Endovascular Therapy, Johns Hopkins Hospital, Baltimore, Maryland
| | - James H. Black
- Department of Vascular Surgery and Endovascular Therapy, Johns Hopkins Hospital, Baltimore, Maryland
| | - Emanuel R. Tenorio
- Department of Cardiothoracic & Vascular Surgery, Advanced Aortic Research Program at the University of Texas Health Science Center at Houston, McGovern Medical School, Houston
| | - Gustavo S. Oderich
- Department of Cardiothoracic & Vascular Surgery, Advanced Aortic Research Program at the University of Texas Health Science Center at Houston, McGovern Medical School, Houston
| | - Zoë Vincent
- Department of Vascular Surgery, Waikato Hospital, University of Auckland, Hamilton, New Zealand
| | - Manar Khashram
- Department of Vascular Surgery, Waikato Hospital, University of Auckland, Hamilton, New Zealand
| | - Matthew J. Eagleton
- Division of Vascular and Endovascular Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Steen Fjord Pedersen
- Division of Vascular Surgery, Department of Cardiovascular Sugery, Aarhus University Hospital, Aarhus, Denmark
| | - Jacob Budtz-Lilly
- Division of Vascular Surgery, Department of Cardiovascular Sugery, Aarhus University Hospital, Aarhus, Denmark
| | - Chiara Lomazzi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Bissacco
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Santi Trimarchi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical and Community Sciences, University of Milan, Milan, Italy
| | - Abigail Huerta
- Vascular Surgery Department, CardioVascular Institute, Hospital Clinic, Barcelona, Spain
| | - Vincent Riambau
- Vascular Surgery Department, CardioVascular Institute, Hospital Clinic, Barcelona, Spain
| | - Anders Wanhainen
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Department of Surgical and Perioperative Sciences, Surgery, Umeå University, Umeå, Sweden
| |
Collapse
|
7
|
Avadhanula V, Creighton C, Ferlic-Stark L, Sucgang R, Zhang Y, Nagaraj D, Nicholson E, Rajan A, Menon V, Doddapaneni H, Muzny D, Metcalf G, Cregeen SJ, Hoffman K, Gibbs R, Petrosino J, Piedra P. Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. Res Sq 2023:rs.3.rs-2978272. [PMID: 37333115 PMCID: PMC10274945 DOI: 10.21203/rs.3.rs-2978272/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
Collapse
|
8
|
Crockett S, Hanna L, Singh A, Gunning S, Nicholas R, Bicknell C, Hamady M, Gable D, Sallam M, Modarai B, Abisi S, Lyons O, Gibbs R. Carbon dioxide flushing versus saline flushing of thoracic aortic stents (INTERCEPTevar): protocol for a multicentre pilot randomised controlled trial. BMJ Open 2023; 13:e067605. [PMID: 37105705 PMCID: PMC10151986 DOI: 10.1136/bmjopen-2022-067605] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/21/2023] [Indexed: 04/29/2023] Open
Abstract
INTRODUCTION Thoracic endovascular aortic repair (TEVAR) carries a 3%-6.1% stroke risk, including risk of 'silent' cerebral infarction (SCI). Stent-grafts are manufactured in room air and retain air. Instructions for use recommend saline flushing to 'de-air' the system prior to insertion, but substantial amounts of air are released when deploying them, potentially leading to downstream neuronal injury and SCI. Carbon dioxide (CO2) is more dense and more soluble in blood than air, without risk of bubble formation, so could be used in addition to saline to de-air stents. This pilot trial aims to assess the feasibility of a full-scale randomised controlled trial (RCT) investigating the neuroprotective benefit against SCI with the use of CO2-flushed aortic stent-grafts. METHODS AND ANALYSIS This is a multicentre pilot RCT, which is taking place in vascular centres in the UK, USA and New Zealand. Patients identified for TEVAR will be enrolled after informed written consent. 120 participants will be randomised (1:1) to TEVAR-CO2 or TEVAR-saline, stratified according to TEVAR landing zone. Participants will undergo preoperative neurocognitive tests and quality of life assessments, which will be repeated at 6 weeks, or first outpatient appointment, and 6 months. Inpatient neurological testing will be performed within 48 hours of return to level 1 care for clinical stroke or delirium. Diffusion-weighted MRI will be undertaken within 72 hours postoperatively (1-7 days) and at 6 months to look for evidence and persistence of SCI. Feasibility will be assessed via measures of recruitment and retention, informing the design of a full-scale trial. ETHICS AND DISSEMINATION The study coordination centre has obtained approval from the London Fulham Research Ethics Committee (19/LO/0836) and Southern Health and Disability Ethics Committee (NZ) and UK's Health Regulator Authority (HRA). The study has received ethical approval for recruitment in the UK (Fulham REC, 19/LO/0836), New Zealand (21/STH/192) and the USA (IRB 019-264, Ref 378630). Consent for entering into the study will be taken using standardised consent forms by the local study team, led by a local PI. The results of the trial will be submitted for publication in an open access journal. TRIAL REGISTRATION NUMBER NCT03886675.
Collapse
Affiliation(s)
- Stephen Crockett
- Department of Surgery and Cancer, Imperial College London, London, UK
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Lydia Hanna
- Department of Surgery and Cancer, Imperial College London, London, UK
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Abhinav Singh
- Neuroradiology Department, Imperial College Healthcare NHS Trust, London, UK
| | - Stephen Gunning
- Clinical Health and Psychology Department, Imperial College Healthcare NHS Trust, London, UK
| | - Richard Nicholas
- Neurology Department, Imperial College Healthcare NHS Trust, London, UK
| | - Colin Bicknell
- Department of Surgery and Cancer, Imperial College London, London, UK
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Mohamad Hamady
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Dennis Gable
- Vascular Surgery Department, Baylor Scott & White Health, Dallas, Texas, USA
| | - Morad Sallam
- Vascular Surgery Department, Guy's and St Thomas' Hospitals NHS Trust, London, UK
| | - Bijan Modarai
- Vascular Surgery Department, Guy's and St Thomas' Hospitals NHS Trust, London, UK
| | - Said Abisi
- Vascular Surgery Department, Guy's and St Thomas' Hospitals NHS Trust, London, UK
| | - Oliver Lyons
- Vascular Surgery Department, Canterbury District Health Board, Christchurch, New Zealand
| | - Richard Gibbs
- Department of Surgery and Cancer, Imperial College London, London, UK
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| |
Collapse
|
9
|
Behera S, Belyeu JR, Chen X, Paulin LF, Nguyen NQH, Newman E, Mahmoud M, Menon VK, Qi Q, Joshi P, Marcovina S, Rossi M, Roller E, Han J, Onuchic V, Avery CL, Ballantyne CM, Rodriguez CJ, Kaplan RC, Muzny DM, Metcalf GA, Gibbs R, Yu B, Boerwinkle E, Eberle MA, Sedlazeck FJ. Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk. bioRxiv 2023:2023.04.24.538128. [PMID: 37163057 PMCID: PMC10168217 DOI: 10.1101/2023.04.24.538128] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase ~50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.
Collapse
Affiliation(s)
- S Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - X Chen
- Illumina Inc., San Diego, CA, USA
| | - L F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - N Q H Nguyen
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | - E Newman
- Illumina Inc., San Diego, CA, USA
| | - M Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - V K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Q Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - P Joshi
- Medpace Reference Laboratories, Cincinnati, OH, USA
| | - S Marcovina
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Rossi
- Illumina Inc., San Diego, CA, USA
| | - E Roller
- Illumina Inc., San Diego, CA, USA
| | - J Han
- Illumina Inc., San Diego, CA, USA
| | | | - C L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - C M Ballantyne
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - C J Rodriguez
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - R C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Fred Hutchinson Cancer Center, Public Health Sciences Division, Seattle WA 98109
| | - D M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - G A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - R Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - B Yu
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | - E Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
| | | | - F J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, USA
| |
Collapse
|
10
|
Jaehnig EJ, Fernandez-Martinez A, Vashist T, Holt MV, Williams L, Lei J, Kim BJ, Dou Y, Korchina V, Gibbs R, Muzny D, Doddapaneni H, Rodriguez H, Robles A, Hiltke T, Mani DR, Gillette M, Hyslop T, Wen Y, McCart L, Miles G, Carr S, Zhang B, Satpathy S, Ellis M, Anurag M. Abstract P5-02-36: Proteogenomic profiling of fresh frozen core biopsies from CALGB 40601. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p5-02-36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: Targeted therapy for HER2+ breast cancer has significantly improved outcomes for this aggressive subtype. However, a subset of patients do not achieve pathological complete response (pCR). In CALGB 40601, a randomized Phase III Trial for neoadjuvant treatment of HER2+ primary breast cancer with Paclitaxel (T: taxane) combined with HER2 antibody therapy (H: Herceptin/Trastuzumab), the small molecule inhibitor Lapatinib (L), or the antibody-inhibitor combination, pCR frequency was 56% for the combination (THL arm), 46% for Trastuzumab (TH arm), and 32% for Lapatinib (TL arm, closed early because of lower efficacy) (PMID: 26527775). While a recent publication reports relapse-free survival (RFS), overall survival (OS), and RNA-based gene expression signatures that can predict pCR (PMID: 33095682), understanding the proteogenomic landscape of treatment response should facilitate identification of alternative and therapeutically tractable protein targets for treatment-resistant tumors. Methods: Microscaled proteogenomic profiling (PMID: 31988290) was performed on treatment-naïve, flash-frozen core needle biopsies from the CALGB 40601 trial obtained from the Alliance for Clinical Trials in Oncology tissue bank. Multi-omics profiling included whole-exome sequencing (WES), RNA-sequencing, and mass spectroscopy-based proteomics and phosphoproteomics from one or two cores from each patient. Results: Eighty baseline core biopsies from 54 patients, including 22 patients from the THL arm, 24 from the TH arm, and 8 from the TL arm, from the CALGB 40601 tissue archive were of sufficient quality to yield genomics, transcriptomics, and/or proteomics profiling data. The frequency of pCR for profiled samples was representative of the overall trial cohort. Linear models were employed to identify baseline determinants of pCR for each arm and to assess differences in genes associated with response between the TH and THL arms. Pathways associated with RNA processing, translation, and the proteasome were elevated in pCR tumors in TH and THL arms, while cell cycle, DNA replication and repair pathways were higher in pCR only in the THL arm. While enrichment of similar pathways was observed in pCR in the transcriptome, the proteome specifically showed enrichment of pathways associated with extracellular matrix and EMT in non-pCR in the THL but not the TH arm. In particular, “EMT”, “ECM-receptor interaction”, and “extracellular structure organization” constituted the most enriched pathways and GO terms that were higher in non-pCR than in pCR tumors from the combination arm (THL) in the proteomics data despite showing no enrichment in the transcriptomics data. Driving this pathway enrichment were several collagens and matrix metalloproteinases that were significantly elevated in non-pCR tumors at the protein but not the RNA level. Finally, kinase target enrichment of differential phosphorylation sites suggested that the activity of PAK1, a regulator of cytoskeletal remodeling, is elevated in non-pCR tumors from the THL arm (p=0.006), but not the TH arm (p=0.69). Conclusion: Proteogenomic analysis of archival HER2+ breast cancer core biopsies provides opportunities for identifying proteins and phosphorylation sites in treatment-naive tumors that are associated with pCR to neoadjuvant Paclitaxel/anti-HER2 therapy. Notably, proteomic but not transcriptomic data showed that ECM and EMT pathways were elevated in non-pCR tumors; thus, signatures encompassing these pathways may serve as biomarkers for aggressive HER2+ breast cancer that is more likely to evade treatment. Non-pCR tumors in the THL arm were also marked by elevated levels of PAK1 target phosphorylation sites, suggesting that this kinase may be a potential therapeutic target in HER2+ breast cancer that is refractory to combination anti-HER2 therapy.
Citation Format: Eric J. Jaehnig, Aranzazu Fernandez-Martinez, Tanmayi Vashist, Matthew V. Holt, LaTerrica Williams, Jonathan Lei, Beom-Jun Kim, Yongchao Dou, Viktoriya Korchina, Richard Gibbs, Donna Muzny, Harshavardhan Doddapaneni, Henry Rodriguez, Ana Robles, Tara Hiltke, DR Mani, Michael Gillette, Terry Hyslop, Yujia Wen, Linda McCart, George Miles, Steven Carr, Bing Zhang, Shankha Satpathy, Matthew Ellis, Meenakshi Anurag. Proteogenomic profiling of fresh frozen core biopsies from CALGB 40601 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-36.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - DR Mani
- 16Broad Institute of MIT and Harvard
| | | | | | - Yujia Wen
- 19Alliance for Clinical Trials in Oncology
| | - Linda McCart
- 20The Ohio State University Wexner Medical Center
| | | | | | | | | | | | | |
Collapse
|
11
|
Einson J, Glinos D, Boerwinkle E, Castaldi P, Darbar D, de Andrade M, Ellinor P, Fornage M, Gabriel S, Germer S, Gibbs R, Hersh CP, Johnsen J, Kaplan R, Konkle BA, Kooperberg C, Nassir R, Loos RJF, Meyers DA, Mitchell BD, Psaty B, Vasan RS, Rich SS, Rienstra M, Rotter JI, Saferali A, Shoemaker MB, Silverman E, Smith AV, Mohammadi P, Castel SE, Iossifov I, Lappalainen T. Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. bioRxiv 2023:2023.01.31.526505. [PMID: 36778406 PMCID: PMC9915611 DOI: 10.1101/2023.01.31.526505] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/16/2023]
Abstract
Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-seq data in GTEx v8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased WGS data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.
Collapse
Affiliation(s)
- Jonah Einson
- Department of Biomedical Informatics, Columbia University
- New York Genome Center
| | | | | | | | - Dawood Darbar
- Department of Cardiology, University of Illinois at Chicago
| | | | - Patrick Ellinor
- Corrigan Minehan Heart Center, Massachusetts General Hospital
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health at Houston
| | | | | | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine Human Genome Sequencing Center
| | - Craig P Hersh
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital
| | - Jill Johnsen
- Department of Hematology, University of Washington
| | - Robert Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine
| | | | | | - Rami Nassir
- Department of Pathology, School of Medicine, Umm Al-Qura University
| | - Ruth J F Loos
- Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai
| | | | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington
| | | | | | | | - 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
| | - Aabida Saferali
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital
| | | | - Edwin Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham & Women's Hospital
| | | | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute
| | | | | | - Tuuli Lappalainen
- Department of Systems Biology, Columbia University
- Department of Gene Technology, KTH Royal Institute of Technology
- New York Genome Center
| |
Collapse
|
12
|
Farek J, Hughes D, Salerno W, Zhu Y, Pisupati A, Mansfield A, Krasheninina O, English AC, Metcalf G, Boerwinkle E, Muzny DM, Gibbs R, Khan Z, Sedlazeck FJ. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments. Gigascience 2022; 12:giac125. [PMID: 36644891 PMCID: PMC9841152 DOI: 10.1093/gigascience/giac125] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/24/2022] [Accepted: 12/08/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The growing volume and heterogeneity of next-generation sequencing (NGS) data complicate the further optimization of identifying DNA variation, especially considering that curated high-confidence variant call sets frequently used to validate these methods are generally developed from the analysis of comparatively small and homogeneous sample sets. FINDINGS We have developed xAtlas, a single-sample variant caller for single-nucleotide variants (SNVs) and small insertions and deletions (indels) in NGS data. xAtlas features rapid runtimes, support for CRAM and gVCF file formats, and retraining capabilities. xAtlas reports SNVs with 99.11% recall and 98.43% precision across a reference HG002 sample at 60× whole-genome coverage in less than 2 CPU hours. Applying xAtlas to 3,202 samples at 30× whole-genome coverage from the 1000 Genomes Project achieves an average runtime of 1.7 hours per sample and a clear separation of the individual populations in principal component analysis across called SNVs. CONCLUSIONS xAtlas is a fast, lightweight, and accurate SNV and small indel calling method. Source code for xAtlas is available under a BSD 3-clause license at https://github.com/jfarek/xatlas.
Collapse
Affiliation(s)
- Jesse Farek
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Hughes
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Institute of Genomic Medicine, Columbia University, New York, NY 10027, USA
| | - William Salerno
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Yiming Zhu
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aishwarya Pisupati
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adam Mansfield
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Olga Krasheninina
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Adam C English
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
13
|
Selvaraj MS, Li X, Li Z, Pampana A, Zhang DY, Park J, Aslibekyan S, Bis JC, Brody JA, Cade BE, Chuang LM, Chung RH, Curran JE, de Las Fuentes L, de Vries PS, Duggirala R, Freedman BI, Graff M, Guo X, Heard-Costa N, Hidalgo B, Hwu CM, Irvin MR, Kelly TN, Kral BG, Lange L, Li X, Lisa M, Lubitz SA, Manichaikul AW, Michael P, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Reupena MS, Smith JA, Sun X, Taylor KD, Tracy RP, Tsai MY, Wang Z, Wang Y, Bao W, Wilkins JT, Yanek LR, Zhao W, Arnett DK, Blangero J, Boerwinkle E, Bowden DW, Chen YDI, Correa A, Cupples LA, Dutcher SK, Ellinor PT, Fornage M, Gabriel S, Germer S, Gibbs R, He J, Kaplan RC, Kardia SLR, Kim R, Kooperberg C, Loos RJF, Viaud-Martinez KA, Mathias RA, McGarvey ST, Mitchell BD, Nickerson D, North KE, Psaty BM, Redline S, Reiner AP, Vasan RS, Rich SS, Willer C, Rotter JI, Rader DJ, Lin X, Peloso GM, Natarajan P. Whole genome sequence analysis of blood lipid levels in >66,000 individuals. Nat Commun 2022; 13:5995. [PMID: 36220816 PMCID: PMC9553944 DOI: 10.1038/s41467-022-33510-7] [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: 09/27/2021] [Accepted: 09/21/2022] [Indexed: 01/05/2023] Open
Abstract
Blood lipids are heritable modifiable causal factors for coronary artery disease. Despite well-described monogenic and polygenic bases of dyslipidemia, limitations remain in discovery of lipid-associated alleles using whole genome sequencing (WGS), partly due to limited sample sizes, ancestral diversity, and interpretation of clinical significance. Among 66,329 ancestrally diverse (56% non-European) participants, we associate 428M variants from deep-coverage WGS with lipid levels; ~400M variants were not assessed in prior lipids genetic analyses. We find multiple lipid-related genes strongly associated with blood lipids through analysis of common and rare coding variants. We discover several associated rare non-coding variants, largely at Mendelian lipid genes. Notably, we observe rare LDLR intronic variants associated with markedly increased LDL-C, similar to rare LDLR exonic variants. In conclusion, we conducted a systematic whole genome scan for blood lipids expanding the alleles linked to lipids for multiple ancestries and characterize a clinically-relevant rare non-coding variant model for lipids.
Collapse
Affiliation(s)
- Margaret Sunitha Selvaraj
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Akhil Pampana
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David Y Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- 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
| | - Lee-Ming Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, 350, Taiwan
| | - 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, 78520, USA
| | - Lisa de Las Fuentes
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, 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
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 78520, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Mariaelisa Graff
- Department of Epidemiology, UNC Chapel Hill, Chapel Hill, NC, 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
| | - Nancy Heard-Costa
- Department of Neurology, Boston university School of Medicine, Boston, MA, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
- Tulane University Translational Science Institute, New Orleans, LA, 70112, USA
| | - Brian G Kral
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiaohui Li
- 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
| | - Martin Lisa
- Department of Medicine, George Washington University, Washingron, DC, USA
| | - Steven A Lubitz
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Ani W Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Preuss Michael
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - May E Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 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
| | - Take Naseri
- Ministry of Health, Government of Samoa, Samoa, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, 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
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, USA
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minneosta, Minneapolis, MN, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Wei Bao
- Institute of Public Health, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - John T Wilkins
- Department of Medicine (Cardiology) and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Donna K Arnett
- Dean's Office, University of Kentucky College of Public Health, Lexington, KY, 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, 78520, 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
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Adolfo Correa
- Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Susan K Dutcher
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 7722, USA
| | | | - Soren Germer
- New York Genome Center, New York, NY, 10013, USA
| | - Richard Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, 77030, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
- Tulane University Translational Science Institute, New Orleans, LA, 70112, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan Kim
- Psomagen, Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- NNF Center for Basic Metabolic Research, University of Copenhagen, Cophenhagen, Denmark
| | | | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Stephen T McGarvey
- Department of Epidemiology, International Health Institute, Brown University, Providence, RI, 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 Nickerson
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Kari E North
- Department of Epidemiology, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, 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, 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Ramachandran S Vasan
- Sections of Preventive medicine and Epidemiology, Cardiovascular medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Cristen Willer
- University of Michigan, Internal Medicine, Ann Arbor, MI, 48109, 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
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xihong Lin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Statistics, Harvard University, Cambridge, MA, 02138, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA.
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
14
|
Ramirez AH, Sulieman L, Schlueter DJ, Halvorson A, Qian J, Ratsimbazafy F, Loperena R, Mayo K, Basford M, Deflaux N, Muthuraman KN, Natarajan K, Kho A, Xu H, Wilkins C, Anton-Culver H, Boerwinkle E, Cicek M, Clark CR, Cohn E, Ohno-Machado L, Schully SD, Ahmedani BK, Argos M, Cronin RM, O’Donnell C, Fouad M, Goldstein DB, Greenland P, Hebbring SJ, Karlson EW, Khatri P, Korf B, Smoller JW, Sodeke S, Wilbanks J, Hentges J, Mockrin S, Lunt C, Devaney SA, Gebo K, Denny JC, Carroll RJ, Glazer D, Harris PA, Hripcsak G, Philippakis A, Roden DM, Ahmedani B, Cole Johnson CD, Ahsan H, Antoine-LaVigne D, Singleton G, Anton-Culver H, Topol E, Baca-Motes K, Steinhubl S, Wade J, Begale M, Jain P, Sutherland S, Lewis B, Korf B, Behringer M, Gharavi AG, Goldstein DB, Hripcsak G, Bier L, Boerwinkle E, Brilliant MH, Murali N, Hebbring SJ, Farrar-Edwards D, Burnside E, Drezner MK, Taylor A, Channamsetty V, Montalvo W, Sharma Y, Chinea C, Jenks N, Cicek M, Thibodeau S, Holmes BW, Schlueter E, Collier E, Winkler J, Corcoran J, D’Addezio N, Daviglus M, Winn R, Wilkins C, Roden D, Denny J, Doheny K, Nickerson D, Eichler E, Jarvik G, Funk G, Philippakis A, Rehm H, Lennon N, Kathiresan S, Gabriel S, Gibbs R, Gil Rico EM, Glazer D, Grand J, Greenland P, Harris P, Shenkman E, Hogan WR, Igho-Pemu P, Pollan C, Jorge M, Okun S, Karlson EW, Smoller J, Murphy SN, Ross ME, Kaushal R, Winford E, Wallace F, Khatri P, Kheterpal V, Ojo A, Moreno FA, Kron I, Peterson R, Menon U, Lattimore PW, Leviner N, Obedin-Maliver J, Lunn M, Malik-Gagnon L, Mangravite L, Marallo A, Marroquin O, Visweswaran S, Reis S, Marshall G, McGovern P, Mignucci D, Moore J, Munoz F, Talavera G, O'Connor GT, O'Donnell C, Ohno-Machado L, Orr G, Randal F, Theodorou AA, Reiman E, Roxas-Murray M, Stark L, Tepp R, Zhou A, Topper S, Trousdale R, Tsao P, Weidman L, Weiss ST, Wellis D, Whittle J, Wilson A, Zuchner S, Zwick ME. The All of Us Research Program: Data quality, utility, and diversity. Patterns 2022; 3:100570. [PMID: 36033590 PMCID: PMC9403360 DOI: 10.1016/j.patter.2022.100570] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 03/30/2022] [Accepted: 07/14/2022] [Indexed: 11/05/2022]
Abstract
The All of Us Research Program seeks to engage at least one million diverse participants to advance precision medicine and improve human health. We describe here the cloud-based Researcher Workbench that uses a data passport model to democratize access to analytical tools and participant information including survey, physical measurement, and electronic health record (EHR) data. We also present validation study findings for several common complex diseases to demonstrate use of this novel platform in 315,000 participants, 78% of whom are from groups historically underrepresented in biomedical research, including 49% self-reporting non-White races. Replication findings include medication usage pattern differences by race in depression and type 2 diabetes, validation of known cancer associations with smoking, and calculation of cardiovascular risk scores by reported race effects. The cloud-based Researcher Workbench represents an important advance in enabling secure access for a broad range of researchers to this large resource and analytical tools. The All of Us Research Program has released data for over 315,000 participants Demonstration projects support the utility and validity of the All of Us dataset The cloud-based Researcher Workbench provides secure, low-cost compute power
The engagement of participants in the research process and broad availability of data to diverse researchers are essential elements in building precision medicine equitably available for all. The NIH has established the ambitious All of Us Research Program to build one of the most diverse health databases in history with tools to support research to improve human health. Here, we present the initial launch of the Researcher Workbench with data types including surveys, physical measurements, and electronic health record data with validation studies to support researcher use of this novel platform. Broad access for researchers to data like these is a critical step in returning value to participants seeking to support the advancement of precision medicine and improved health for all.
Collapse
|
15
|
Hanna L, Lam K, Agbeko A, Amoako J, Ashrafian H, Sounderajah V, Abdullah A, Gibbs R. Coverage of the Coeliac Artery During Thoracic Endovascular Aortic Repair: A Systematic Review and Meta-Analysis. J Vasc Surg 2022. [DOI: 10.1016/j.jvs.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
16
|
Sahid S, Daurka J, Gibbs R, Murphy J. O094 Novel technique and cohort study: Stoppa approach to sciatic notch clearance in locally advanced / recurrent pelvic cancer pelvic cancer. Br J Surg 2022. [DOI: 10.1093/bjs/znac242.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract
Introduction
Locally advanced / recurrent pelvic cancers (LARC) extending into the greater sciatic notch represent a significant clinical challenge. Conventional surgical resection is associated with high rates of R1/2 resection, while locoregional oncological treatments often fail to control the disease. In this study we present the first report of a modified Stoppa approach that facilitates en bloc excision of pelvic sidewall structures with LARC.
Methods
This is a retrospective review of patients who underwent surgery for LARC with the novel Stoppa approach between 2016 and 2020 in our centre.
Result
7 patients (6 female and 1 male) were identified from the institutional database with Median age of 66 (37–74). Three separate tumour types were included in the cohort: rectal adenocarcinoma - 4 (57%), anal squamous cell carcinoma - 2 (29%), and prostate adenocarcinoma - 1 (14%). 3 (42%) patients developed Clavien Dindo Class III complications (2 returned to theatre for minor flap revisions; 1 pre-sacral collection required radiological drainage). All patients lost active ipsilateral foot dorsiflexion due to planned nerve root transection. Median hospital stay was 46 days (17–114). All resections were R0.
Conclusion
This is the first report of a novel Stoppa approach for en bloc pelvic sidewall excision. The presented pathological resection results are promising; however, this procedure is associated with significant morbidity. Future studies will be necessary to confirm the presented oncological results and determine if the associated morbidity can be decreased.
Take-home message
Modified Stoppa technique is feasible to achieve Sciatic Notch tumour clearance in primary or recurrent locally advanced pelvic cancer. Further research needed to assess long term oncological outcome and reduce post operative morbidity.
Collapse
Affiliation(s)
- S Sahid
- Department of Surgery and Cancer, Imperial College Healthcare NHS Trust
| | - J Daurka
- Department of Orthopaedics, Imperial College Healthcare NHS Trust
| | - R Gibbs
- Division of Vascular Medicine and Vascular Surgery, Imperial College Healthcare NHS
| | - J Murphy
- Department of Surgery and Cancer, Imperial College Healthcare NHS Trust
| |
Collapse
|
17
|
Yang QZC, Hanna L, Statton B, Armour C, ORegan D, Xu Y, Gibbs R. O024 Prognostic value of haemodynamic parameters in predicting adverse clinical events in type B aortic dissection. Br J Surg 2022. [DOI: 10.1093/bjs/znac242.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Introduction
Ascertain the prognostic role of in-vivo 4D-flow magnetic resonance imaging (MRI) and computational fluid dynamics (CFD) aortic haemodynamic parameters as predictors of adverse dissection-related events in type B aortic dissection (TBAD).
Methods
A systematic literature search was conducted according to the PRISMA guidelines using electronic databases searched from 1946 to 2021 for studies reporting on the relationship between aortic haemodynamics and aortic dissection-related events defined as aortic growth, aneurysm development, false lumen thrombosis, need for surgery and aortic rupture.
Results
Fourteen studies were included; eleven studies used CFD and three studies used 4D-flow MRI. Two studies found increased FL ejection fraction (EF) significantly associated with aortic growth rate, and another study found increased FL stroke volume significantly associated with increased aortic expansion rate. Result for time-averaged wall shear stress (TAWSS) and relative residence time (RRT) are contradictory; one study found TAWSS significantly associated with aortic wall deformation, but another study found no significant difference. Five studies suggested possible associations between slow flowing regions or increased RRT and FL thrombosis, with another study finding significant associations between FL thrombosis and adverse aortic outcomes. However, one study revealed opposite findings where decreased RRT significantly correlated with aneurysm formation.
Conclusion
In-vivo aortic haemodynamic measurements such as FL EF, FL stroke volume, TAWSS and RRT show possible associations with FL and aortic expansion, as well as FL thrombosis. Larger prospective studies are now needed to determine the prognostic utility of in vivo aortic haemodynamic metrics in predicting TBAD clinical outcomes to guide management.
Take-home message
Aortic haemodynamic parameters measured by 4D-flow magnetic resonance imaging and computational fluid dynamics show promising potential as predictors of adverse dissection-related events in type B aortic dissection.
Collapse
Affiliation(s)
- QZC Yang
- School of Medicine, Imperial College London
| | - L Hanna
- Department of Surgery and Cancer, Imperial College London
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust
| | - B Statton
- MRC London Institute of Medical Sciences, Imperial College London
| | - C Armour
- Department of Chemical Engineering, Imperial College London
| | - D ORegan
- MRC London Institute of Medical Sciences, Imperial College London
| | - Y Xu
- Department of Chemical Engineering, Imperial College London
| | - R Gibbs
- Department of Surgery and Cancer, Imperial College London
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust
| |
Collapse
|
18
|
Ellis MJ, Anurag M, Hoog J, Fernandez-Martinez A, Fan C, Gibbs R, Sanati S, Vij K, Watson M, Dockter T, Hahn O, Guenther J, Caudle A, Crouch E, Tiersten A, Mita M, Razaq W, Hieken TJ, Wang Y, Leitch AM, Unzeitig GW, Winer E, Weiss A, Hunt K, Partridge AH, Perou CM, Suman V, Ma CX, Carey LA. Abstract CT026: The effect of intrinsic subtype on inhibition of tumor growth by anastrozole vs. fulvestrant vs. the combination: Results from the Alliance neoadjuvant endocrine therapy (NET) ALTERNATE trial. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-ct026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: The ALTERNATE trial randomized postmenopausal women with ER Allred 6-8 HER2- breast cancer to 6 months of NET with anastrozole (A), fulvestrant (F) or the combination (A+F). Biopsies were taken preNET and after 4-weeks(wks). Patients with Ki67 values >10% at 4-wks were offered triage to neoadjuvant chemotherapy. Patients with on-treatment Ki67 ≤ 10% who completed NET underwent surgery and Ki67 was reassessed. The primary endpoint was endocrine-sensitive disease rate (ESDR). ESD is defined as pCR or PEPI-0 residual disease (pT1-2, pN0, Ki67 ≤ 2.7%). We previously reported that the ESDR difference between the F-containing arms and the A arm was not >10% (ASCO 2020) and that baseline RNA-seq-based intrinsic subtypes predicted outcomes overall (SABCS 2021). Herein we describe relationships between PAM50 intrinsic subtype and Ki67 values by treatment arm because comparative drug effectiveness in adjuvant endocrine therapy studies in ER+ HER2- breast cancer can be predicted by the degree of Ki67 suppression (PMC3518447).
Methods: 743 of the 1297 eligible patients (A: 264; F: 231; A+F: 248) had RNA extracted from preNET frozen tumor biopsies with >50% tumor content and subjected to RNA seq. Intrinsic subtypes were then assigned as LumA, LumB, and NonLum (Basal or HER2-E) using open-source PAM50-based informatics. Differences in the proportion with wk4 Ki67 > 10%, % change in wk4 ki67, and surgical CCCA (Ki67 ≤ 2.7%) rate (sxCCCA) between treatments and by intrinsic subtype was assessed using stratified logistic regression, Wilcoxon rank sum test, and Fisher’s exact test, respectively. Analysis of sxCCCA excluded those who failed to complete NET for reasons other than disease progression or early Ki67 >10%.
Results: Amongst the 358 LumA cases there were no significant differences in Ki67-based endpoints between treatments. Among the 292 LumB cases, the wk4 ki67 > 10% rate was lower with A+F (19.4%) than A (43%) (P=0.0002) and was somewhat lower in F (31%) versus A (P=0.076). The % change in wk4 Ki67 in LumB cases, adjusted for baseline Ki67, showed markedly superior suppression for A+F versus A (-90% vs. -77%; P=<0.0001) and versus F (-90% vs. -80%; P=0.0026). Furthermore sxCCCA rates were significantly higher with A+F than A (53% vs. 25% P = <0.0001) and somewhat higher for F (37%) than A (p=0.068), indicating that superior antiproliferative effects for A+F persist after 6 months on therapy. Lack of Ki67 suppression in response to treatment was observed in the majority of 43 NonLum samples regardless of treatment.
Conclusion: The combination of A+F was significantly more effective than either drug alone for the control of LumB breast cancer cell proliferation. This suggests that A+F may be a more effective adjuvant endocrine therapy than A alone in LumB disease. The lower Ki67 suppression with A alone also suggests that poorer outcome in some LumB tumors may be due to insufficient ER targeting rather than ER-independent tumor growth
Support: U10CA180821, U10CA180882, U24CA196171, UG1CA189856, U10CA180868 (NRG), NCI BIQSFP, BCRF, Genentech, AstraZeneca. https://acknowledgments.alliancefound.org. (MJE) CPRIT RR140033, P50-CA186784, P50-CA58223, U01-CA214125, U24-CA210954, Gift from Ralph and Lisa Eads, McNair Scholarship.
ClinicalTrials.gov Identifier: NCT01953588
Citation Format: Matthew J. Ellis, Meenakshi Anurag, Jeremy Hoog, Aranzazu Fernandez-Martinez, Cheng Fan, Richard Gibbs, Souzan Sanati, Kiran Vij, Mark Watson, Travis Dockter, Olwen Hahn, Joseph Guenther, Abigail Caudle, Erica Crouch, Amy Tiersten, Monica Mita, Wajeeha Razaq, Tina J. Hieken, Yang Wang, A. Marilyn Leitch, Gary W. Unzeitig, Eric Winer, Anna Weiss, Kelly Hunt, Ann H. Partridge, Charles M. Perou, Vera Suman, Cynthia X. Ma, Lisa A. Carey. The effect of intrinsic subtype on inhibition of tumor growth by anastrozole vs. fulvestrant vs. the combination: Results from the Alliance neoadjuvant endocrine therapy (NET) ALTERNATE trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT026.
Collapse
Affiliation(s)
| | | | - Jeremy Hoog
- 2Washington University School of Medicine, St. Louis, MO
| | | | - Cheng Fan
- 3University of North Carolina, Chapel Hill, NC
| | | | | | - Kiran Vij
- 2Washington University School of Medicine, St. Louis, MO
| | - Mark Watson
- 2Washington University School of Medicine, St. Louis, MO
| | - Travis Dockter
- 5Alliance Statistics and Data Center and Mayo Clinic, Rochester, MN
| | | | | | | | - Erica Crouch
- 2Washington University School of Medicine, St. Louis, MO
| | | | - Monica Mita
- 4Cedars-Sinai Medical Center, Los Angeles, CA
| | - Wajeeha Razaq
- 10University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | - Yang Wang
- 12Presbyterian Kaseman Hospital, Albuquerque, NM
| | | | | | - Eric Winer
- 15Dana-Farber Cancer Institute, Boston, MA
| | - Anna Weiss
- 15Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | - Vera Suman
- 5Alliance Statistics and Data Center and Mayo Clinic, Rochester, MN
| | - Cynthia X. Ma
- 2Washington University School of Medicine, St. Louis, MO
| | | |
Collapse
|
19
|
Plon S, Desrosiers L, Robinson J, Russell H, Scollon S, Dai H, Raesz-Martinez R, Recinos A, Reuther J, Naik M, Miles G, Ramamurthy U, Muzny D, Roy A, Gibbs R, Tomlinson G, Bernini JC, Gill J, Griffin T, Vallance K, McGuire A, Parsons DW. OP011: Physician recommendations after germline sequencing in pediatric cancer patients: Texas KidsCanSeq study. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
20
|
Ma CX, Anurag M, Dockter T, Hoog J, Fernandez-Martinez A, Fan C, Gibbs R, Sanati S, Vij K, Watson M, Hahn O, Guenther J, Caudle A, Crouch E, Tiersten A, Mita M, Razaq W, Hieken TJ, Wang Y, Leitch AM, Unzeitig GW, Weiss A, Winer EP, Hunt K, Partridge AH, Carey LA, Perou CM, Ellis MJ, Suman V. Abstract PD9-03: Pam50 intrinsic subtype and risk of recurrence score (ROR) for the prediction of endocrine (ET) sensitivity and pathologic response to chemotherapy in postmenopausal women with clinical stage II/III estrogen receptor positive (ER+) and HER2 negative (HER2-) breast cancer (BC) in the alternate trial (Alliance A011106). Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-pd9-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Neoadjuvant ET (NET) offers an opportunity to assess ET sensitivity for ER+ HER2- BC and potentially to tailor therapy. Ki67 >10% on biopsy after 2-4 weeks (wks) of NET identifies patients (pts) with intrinsic ET resistance; while pathologic complete response (pCR) and modified preoperative endocrine prognostic index of 0 (mPEPI 0: pT1-2N0, Ki67 ≤2.7%) at surgery indicates sensitivity to ET. However, on-NET biopsy is not always acceptable or feasible and delays the ET sensitivity determination. PAM50 ROR score and intrinsic subtypes by tumor RNA profiling are prognostic in pts with early stage ER+ HER2- BC, and predict pCR rates to neoadjuvant chemotherapy (NCT) (PMC2667820). We therefore hypothesized that PAM50 analysis on pre-NET biopsies could predict the likelihood of a) a high on-NET Ki67, b) mPEPI-0 or pCR at surgery and, c) pCR for pts triaged to NCT. Methods: The ALTERNATE trial is a phase III study that randomized postmenopausal pts with clinical stage II/III ER+ (Allred score 6-8) HER2- BC to receive neoadjuvant anastrozole, fulvestrant, or both for 6 months before surgery. Research biopsy was required at pre-NET and wk 4, then optional at wk 12. Pts with Ki67 >10% on biopsy at wk 4 or 12 discontinued NET and were offered NCT. PAM50 intrinsic subtype and ROR-P values were generated from mRNA sequencing (RNASeq) analysis on pre-NET biopsies using open-source informatics (PMC7723687) and evaluated for prediction of on-NET Ki67 >10% at wk 4 or 12, pCR or mPEPI-0 post NET, and pCR post NCT. Results: 749 of 1,297 eligible trial pts were included in the analyses, after excluding 548 pts due to insufficient pre-NET tumor for RNASeq (n=511) or PAM50 normal subtype (n=37). Similar to the entire ALTERNATE population, the rate of Ki67 >10% at wk 4 or 12 was 24.4% (95% CI: 21.4-27.7%) and the rate of mPEPI-0/pCR post NET was 19.8% (95% CI: 17.0-22.8%). There were 393 (52.5%) Lum A, 302 (40.3%) Lum B, and 54 (7.2%) non-Lum (9 Basal, 45 HER2-E) BCs. These included 196 (26.2%) ROR-P low, 354 (47.3%) ROR-P medium and 199 (26.6%) ROR-P high BCs. Both the rates of Ki67 >10% at wk 4 or 12 and mPEPI-0/pCR differed significantly with respect to PAM50 subtype or ROR-P category, such that Lum A or ROR-P low BCs were least likely to have a Ki67 >10% at wk 4 or 12 and most likely to achieve mPEPI-0/pCR (Table).
93 of 168 (55.4%) pts triaged to NCT had RNA-seq results, yielding 26 Lum A, 49 Lum B, 4 Basal and 14 HER2-E, with the pCR rates of 0%, 6.1%, 0%, and 21.4%, respectively. There were 10 ROR-P low, 39 medium, and 44 high tumors, with a pCR rate of 0%, 5.1% and 9.1%, respectively. Conclusion: These data indicate that both baseline ROR-P and intrinsic subtype are predictive of early on-NET Ki67 > 10% and mPEPI 0/pCR at surgery after NET. For pts triaged to NCT based on an early on-NET Ki67 >10%, the HER2-E group had the highest pCR rate (20%) and no pCRs were observed in Lum A. These data may be useful for directing neoadjuvant therapy in postmenopausal pts with ER+ HER2- BC. Support: U10CA180821, U10CA180882, U24CA196171, UG1CA189856, U10CA180868 (NRG), NCI BIQSFP, BCRF, Genentech, AstraZeneca. https://acknowledgments.alliancefound.org. (MJE) CPRIT RR140033, P50CA186784, P50-CA58223, U01 CA214125, U24CA210954, Gift from Ralph and Lisa Eads, McNair Scholarship. Trials.gov Identifier: NCT01953588.
Table 1.Rates of Ki67 >10% and mPEPI-0/pCR post NET by PAM50 subtype and ROR-P categoryKi67 >10% at wk 4 or 12mPEPI 0/pCR post NETPAM50 SubtypenYes, n (%)PnNo, n (%)PLum A37251 (13.7%) 95% CI: 10.4-17.6%<0.0001393104 (26.5%) 95%CI: 22.2-31.1%<0.0001Lum B29394 (32.1%) 95% CI: 26.8-37.8%30243 (14.2%) 95%CI: 10.5-18.7%Non-luminal (Basal and HER2-E)5338 (71.7%) 95%CI: 57.6-83.2%541 (1.9%) 95%CI: 0.05-9.9%ROR-P CategorynYes, n (%)PnNo, n (%)PLow18018 (10.0%) 95%CI: 6.0-15.3%<0.000119660 (30.6%) 95%CI: 24.2-37.6%<0.0001Intermediate34474 (21.5%) 95%CI: 17.3-26.2%35471 (20.1%) 95%CI: 16.0-24.6%High19491 (46.9%) 95%CI: 39.7-54.2%19917 (8.5%) 95%CI: 5.1-13.3%
Citation Format: Cynthia X Ma, Meenakshi Anurag, Travis Dockter, Jeremy Hoog, Aranzazu Fernandez-Martinez, Cheng Fan, Richard Gibbs, Souzan Sanati, Kiran Vij, Mark Watson, Olwen Hahn, Joseph Guenther, Abigail Caudle, Erika Crouch, Amy Tiersten, Monica Mita, Wajeeha Razaq, Tina J Hieken, Yang Wang, A. Marilyn Leitch, Gary W Unzeitig, Anna Weiss, Eric P Winer, Kelly Hunt, Ann H Partridge, Lisa A Carey, Charles M Perou, Matthew J Ellis, Vera Suman. Pam50 intrinsic subtype and risk of recurrence score (ROR) for the prediction of endocrine (ET) sensitivity and pathologic response to chemotherapy in postmenopausal women with clinical stage II/III estrogen receptor positive (ER+) and HER2 negative (HER2-) breast cancer (BC) in the alternate trial (Alliance A011106) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD9-03.
Collapse
Affiliation(s)
- Cynthia X Ma
- Washington University School of Medicine, St. Louis, MO
| | | | - Travis Dockter
- Alliance Statistics and Data Center/Mayo Clinic, Rochester, MN
| | - Jeremy Hoog
- Washington University School of Medicine, St. Louis, MO
| | | | - Cheng Fan
- University of North Carolina, Chapel Hill, NC
| | | | | | - Kiran Vij
- Washington University School of Medicine, St. Louis, MO
| | - Mark Watson
- Washington University School of Medicine, St. Louis, MO
| | | | | | | | - Erika Crouch
- Washington University School of Medicine, St. Louis, MO
| | | | - Monica Mita
- Cedars-Sinai Medical Center, Los Angelos, CA
| | - Wajeeha Razaq
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | - Yang Wang
- Presbyterian Kaseman Hospital, Albuquerque, NM
| | | | | | - Anna Weiss
- Dana-Farber Cancer Institute/Partners Cancer Care, Boston, MA
| | - Eric P Winer
- Dana-Farber Cancer Institute/Partners Cancer Care, Boston, MA
| | | | - Ann H Partridge
- Dana-Farber Cancer Institute/Partners Cancer Care, Boston, MA
| | - Lisa A Carey
- Alliance Statistics and Data Center/Mayo Clinic, Rochester, MN
| | | | | | - Vera Suman
- Alliance Statistics and Data Center/Mayo Clinic, Rochester, MN
| |
Collapse
|
21
|
Ferrat LA, Vehik K, Sharp SA, Lernmark Å, Rewers MJ, She JX, Ziegler AG, Toppari J, Akolkar B, Krischer JP, Weedon MN, Oram RA, Hagopian WA, Barbour A, Bautista K, Baxter J, Felipe-Morales D, Driscoll K, Frohnert BI, Stahl M, Gesualdo P, Hoffman M, Karban R, Liu E, Norris J, Peacock S, Shorrosh H, Steck A, Stern M, Villegas E, Waugh K, Simell OG, Adamsson A, Ahonen S, Åkerlund M, Hakola L, Hekkala A, Holappa H, Hyöty H, Ikonen A, Ilonen J, Jäminki S, Jokipuu S, Karlsson L, Kero J, Kähönen M, Knip M, Koivikko ML, Koskinen M, Koreasalo M, Kurppa K, Kytölä J, Latva-aho T, Lindfors K, Lönnrot M, Mäntymäki E, Mattila M, Miettinen M, Multasuo K, Mykkänen T, Niininen T, Niinistö S, Nyblom M, Oikarinen S, Ollikainen P, Othmani Z, Pohjola S, Rajala P, Rautanen J, Riikonen A, Riski E, Pekkola M, Romo M, Ruohonen S, Simell S, Sjöberg M, Stenius A, Tossavainen P, Vähä-Mäkilä M, Vainionpää S, Varjonen E, Veijola R, Viinikangas I, Virtanen SM, Schatz D, Hopkins D, Steed L, Bryant J, Silvis K, Haller M, Gardiner M, McIndoe R, Sharma A, Anderson SW, Jacobsen L, Marks J, Towe PD, Bonifacio E, Gezginci C, Heublein A, Hohoff E, Hummel S, Knopff A, Koch C, Koletzko S, Ramminger C, Roth R, Schmidt J, Scholz M, Stock J, Warncke K, Wendel L, Winkler C, Agardh D, Aronsson CA, Ask M, Bennet R, Cilio C, Dahlberg S, Engqvist H, Ericson-Hallström E, Fors AB, Fransson L, Gard T, Hansen M, Jisser H, Johansen F, Jonsdottir B, Elding Larsson H, Lindström M, Lundgren M, Maziarz M, Månsson-Martinez M, Melin J, Mestan Z, Nilsson C, Ottosson K, Rahmati K, Ramelius A, Salami F, Sjöberg A, Sjöberg B, Törn C, Wimar Å, Killian M, Crouch CC, Skidmore J, Chavoshi M, Meyer A, Meyer J, Mulenga D, Powell N, Radtke J, Romancik M, Roy S, Schmitt D, Zink S, Becker D, Franciscus M, Smith MDE, Daftary A, Klein MB, Yates C, Austin-Gonzalez S, Avendano M, Baethke S, Burkhardt B, Butterworth M, Clasen J, Cuthbertson D, Eberhard C, Fiske S, Garmeson J, Gowda V, Heyman K, Hsiao B, Karges C, Laras FP, Li Q, Liu S, Liu X, Lynch K, Maguire C, Malloy J, McCarthy C, Parikh H, Remedios C, Shaffer C, Smith L, Smith S, Sulman N, Tamura R, Tewey D, Toth M, Uusitalo U, Vijayakandipan P, Wood K, Yang J, Yu L, Miao D, Bingley P, Williams A, Chandler K, Kelland I, Khoud YB, Zahid H, Randell M, Chavoshi M, Radtke J, Zink S, Ke S, Mulholland N, Rich SS, Chen WM, Onengut-Gumuscu S, Farber E, Pickin RR, Davis J, Davis J, Gallo D, Bonnie J, Campolieto P, Petrosino JF, Ajami NJ, Lloyd RE, Ross MC, O’Brien JL, Hutchinson DS, Smith DP, Wong MC, Tian X, Ayvaz T, Tamegnon A, Truong N, Moreno H, Riley L, Moreno E, Bauch T, Kusic L, Metcalf G, Muzny D, Doddapaneni H, Gibbs R, Bourcier K, Briese T, Johnson SB, Triplett E, Ziegler AG, Tamura R, Norris J, Virtanen SM, Frohnert BI, Gesualdo P, Koreasalo M, Miettinen M, Niinistö S, Riikonen A, Silvis K, Hohoff E, Hummel S, Winkler C, Aronsson CA, Skidmore J, Smith MDE, Butterworth M, Li Q, Liu X, Tamura R, Uusitalo U, Yang J, Rich SS, Norris J, Steck A, Ilonen J, Ziegler AG, Törn C, Li Q, Liu X, Parikh H, Erlich H, Chen WM, Onengut-Gumuscu S, Schatz D, Ziegler AG, Cilio C, Bonifacio E, Knip M, Schatz D, Burkhardt B, Lynch K, Yu L, Bingley P, Bourcier K, Hyöty H, Triplett E, Lloyd R, Gesualdo P, Waugh K, Lönnrot M, Agardh D, Cilio C, Larsson HE, Killian M, Burkhardt B, Lynch K, Briese T, Waugh K, Schatz D, Killian M, Johnson SB, Roth R, Baxter J, Driscoll K, Schatz D, Stock J, Fiske S, Liu X, Lynch K, Smith L, Baxter J, Lernmark Å, Baxter J, Killian M, Bautista K, Gesualdo P, Hoffman M, Karban R, Norris J, Waugh K, Adamsson A, Kähönen M, Niininen T, Stenius A, Varjonen E, Hopkins D, Steed L, Bryant J, Gardiner M, Marks J, Ramminger C, Stock J, Winkler C, Aronsson CA, Jonsdottir B, Melin J, Killian M, Crouch CC, Mulenga D, McCarthy C, Smith L, Smith S, Tamura R, Johnson SB, Agardh D, Liu E, Koletzko S, Kurppa K, Stahl M, Hoffman M, Kurppa K, Lindfors K, Simell S, Steed L, Aronsson CA, Killian M, Tamura R, Haller M, Larsson HE, Frohnert BI, Gesualdo P, Hoffman M, Steck A, Kähönen M, Veijola R, Steed L, Jacobsen L, Marks J, Stock J, Warncke K, Lundgren M, Wimar Å, Crouch CC, Liu X, Tamura R. Author Correction: A combined risk score enhances prediction of type 1 diabetes among susceptible children. Nat Med 2022; 28:599. [DOI: 10.1038/s41591-021-01631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
22
|
Ting A, Barnetson C, Joegi A, Gibbs R. 595 Penetrating Pelvic Trauma from a Crossbow Bolt: An Unusual Choice of Weapon. Br J Surg 2021. [DOI: 10.1093/bjs/znab259.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Introduction
The crossbow was a popular weapon in medieval times due to their relative ease of use and accuracy but was superseded by firearms around the 16th century. Today, it is legal for adults in the UK to own a crossbow without a licence.
Case Report
A young adult male victim was brought to a Major Trauma Centre with a single lower left quadrant penetrating wound caused a crossbow bolt that was self-removed immediately after the injury. A 2.5cm entry wound was present with no exit wound. The patient was haemodynamically unstable on arrival and was transferred to theatre without imaging within 16 minutes of arrival. The main operative findings were multiple small bowel serosal tears, a full thickness small bowel injury with no contamination and a left external iliac artery injury with active bleeding which were all repaired primarily. The post-operative recovery course included occlusive left cephalic and antecubital vein thrombi and an extensive non-occlusive left common femoral vein thrombus treated with anticoagulant therapy but was otherwise unremarkable. He was discharged 10 days later with no lasting sequelae at 6-week follow up.
Discussion
This case highlights a rare but important and likely underreported modality of penetrating injury. Crossbow bolts have low kinetic energy compared to bullets but high penetrative force, thus little energy is transferred to surrounding tissues. Hence the main injuries caused by crossbow bolts are due to direct damage to structures they come into contact with. Although rare, trauma surgeons should be aware of the pattern of injury caused by crossbows.
Collapse
Affiliation(s)
- A Ting
- Imperial College London, London, United Kingdom
| | | | - A Joegi
- Imperial College London, London, United Kingdom
| | - R Gibbs
- St Mary's Hospital, London, United Kingdom
| |
Collapse
|
23
|
Jun G, Sedlazeck F, Zhu Q, English A, Metcalf G, Kang HM, Lee C, Gibbs R, Boerwinkle E. muCNV: Genotyping Structural Variants for Population-level Sequencing. Bioinformatics 2021; 37:btab199. [PMID: 33760063 PMCID: PMC8496513 DOI: 10.1093/bioinformatics/btab199] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/31/2021] [Accepted: 03/13/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION There are high demands for joint genotyping of structural variations with short-read sequencing, but efficient and accurate genotyping in population scale is a challenging task. RESULTS We developed muCNV that aggregates per-sample summary pileups for joint genotyping of > 100,000 samples. Pilot results show very low Mendelian inconsistencies. Applications to large-scale projects in cloud show the computational efficiencies of muCNV genotyping pipeline. AVAILABILITY muCNV is publicly available for download at: https://github.com/gjun/muCNV. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Goo Jun
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Fritz Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Adam English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| |
Collapse
|
24
|
Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee SB, Tian X, Browning BL, Das S, Emde AK, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, Barr RG, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen YDI, Cho MH, Choi SH, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, de Andrade M, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin KH, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, Mak ACY, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers DA, Mikulla JL, Minear MA, Mitchell BD, Mohanty S, Montasser ME, Montgomery C, Morrison AC, Murabito JM, Natale A, Natarajan P, Nelson SC, North KE, O'Connell JR, Palmer ND, Pankratz N, Peloso GM, Peyser PA, Pleiness J, Post WS, Psaty BM, Rao DC, Redline S, Reiner AP, Roden D, Rotter JI, Ruczinski I, Sarnowski C, Schoenherr S, Schwartz DA, Seo JS, Seshadri S, Sheehan VA, Sheu WH, Shoemaker MB, Smith NL, Smith JA, Sotoodehnia N, Stilp AM, Tang W, Taylor KD, Telen M, Thornton TA, Tracy RP, Van Den Berg DJ, Vasan RS, Viaud-Martinez KA, Vrieze S, Weeks DE, Weir BS, Weiss ST, Weng LC, Willer CJ, Zhang Y, Zhao X, Arnett DK, Ashley-Koch AE, Barnes KC, Boerwinkle E, Gabriel S, Gibbs R, Rice KM, Rich SS, Silverman EK, Qasba P, Gan W, Papanicolaou GJ, Nickerson DA, Browning SR, Zody MC, Zöllner S, Wilson JG, Cupples LA, Laurie CC, Jaquish CE, Hernandez RD, O'Connor TD, Abecasis GR. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 2021; 590:290-299. [PMID: 33568819 PMCID: PMC7875770 DOI: 10.1038/s41586-021-03205-y] [Citation(s) in RCA: 801] [Impact Index Per Article: 267.0] [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: 03/06/2019] [Accepted: 01/07/2021] [Indexed: 02/08/2023]
Abstract
The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.
Collapse
Affiliation(s)
- Daniel Taliun
- 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
| | - Daniel N Harris
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael D Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jedidiah Carlson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA
| | - Raul Torres
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah A Gagliano Taliun
- 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
| | | | | | - Hyun Min Kang
- 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
| | | | - Jonathon LeFaive
- 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
| | - Seung-Been Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaowen Tian
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Brian L Browning
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sayantan Das
- 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
| | | | | | - Douglas P Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 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
| | - 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
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Xiaoming Liu
- USF Genomics, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Dean M Bobo
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI, USA
| | | | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
| | | | | | - Rebecca L Beer
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emelia J Benjamin
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Michael Boehnke
- 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
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Department of Medicine, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian E Cade
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - James F Casella
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
- Division of Pediatric Hematology, Johns Hopkins University, Baltimore, MD, USA
| | - Brandon Chalazan
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Mina K Chung
- Department of Cardiovascular Medicine, Heart & Vascular Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Clary B Clish
- Metabolomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, 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
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Susan K Dutcher
- McDonnell Genome Institute, Washington University, St Louis, MO, USA
- Department of Genetics, Washington University, St Louis, MO, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Diane Fatkin
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales, Australia
| | - Tasha Fingerlin
- National Jewish Health, Center for Genes, Environment and Health, Denver, CO, USA
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christian Fuchsberger
- 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
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Mark T Gladwin
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel J Gottlieb
- VA Boston Healthcare System, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael E Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jiang He
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
- Tulane University Translational Science Institute, Tulane University, New Orleans, LA, USA
| | - Nancy L Heard-Costa
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jill M Johnsen
- Department of Medicine, University of Washington, Seattle, WA, USA
- Bloodworks Northwest Research Institute, Seattle, WA, USA
| | - Andrew D Johnson
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA, USA
| | - Robert Kaplan
- Albert Einstein College of Medicine, New York, NY, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Tanika Kelly
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Shannon Kelly
- Department of Epidemiology, Vitalant Research Institute, San Francisco, CA, USA
- Department of Pediatrics, UCSF Benioff Children's Hospital, Oakland, CA, USA
- Division of Pediatric Hematology, UCSF Benioff Children's Hospital, Oakland, CA, USA
| | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas P Kiel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert Klemmer
- 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
| | - Barbara A Konkle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Bloodworks Northwest Research Institute, Seattle, WA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Leslie A Lange
- Department of Medicine, University of Colorado at Denver, Aurora, CO, USA
| | - Jessica Lasky-Su
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA, USA
| | - Xihong Lin
- Biostatistics and Statistics, Harvard University, Boston, MA, USA
| | - Keng-Han Lin
- 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
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 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
| | - Lori Garman
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | | | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David D McManus
- Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stephen T McGarvey
- International Health Institute, Brown University, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
- Department of Anthropology, Brown University, Providence, RI, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Harvard Medical School, The Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Julie L Mikulla
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mollie A Minear
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Braxton D Mitchell
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- 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
| | - Sanghamitra Mohanty
- Texas Cardiac Arrhythmia Institute, St David's Medical Center, Austin, TX, USA
- Department of Internal Medicine, Dell Medical School, Austin, TX, USA
| | - May E Montasser
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Courtney Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Alanna C Morrison
- 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
| | - Joanne M Murabito
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrea Natale
- Texas Cardiac Arrhythmia Institute, St David's Medical Center, Austin, TX, USA
| | - Pradeep Natarajan
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey R O'Connell
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jacob Pleiness
- 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
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Bruce M Psaty
- Department of Medicine, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - D C Rao
- Division of Biostatistics, Washington University in St Louis, St Louis, MO, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Jeong-Sun Seo
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Macrogen Inc, Seoul, Republic of Korea
- Gong Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center at San Antonio, San Antonio, TX, USA
| | - Vivien A Sheehan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Wayne H Sheu
- Taichung Veterans General Hospital Taiwan, Taichung City, Taiwan
| | | | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | | | - Russell P Tracy
- Department of Pathology & Laboratory Medicine, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - David J Van Den Berg
- Center for Genetic Epidemiology, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ramachandran S Vasan
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | | | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, 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
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Scott T Weiss
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine-Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Yingze Zhang
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xutong Zhao
- 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
| | - Donna K Arnett
- Department of Epidemiology, University of Kentucky, Lexington, KY, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Boerwinkle
- University of Texas Health Science Center at Houston, Houston, TX, USA
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Stacey Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pankaj Qasba
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - George J Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Northwest Genomics Center, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Sebastian Zöllner
- 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
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Framingham Heart Study, Framingham, MA, USA.
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Cashell E Jaquish
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
| |
Collapse
|
25
|
Igbinosa I, Lee K, Oakeson A, Riley E, Melchor S, Birdsong J, Tran L, Weng Y, Collins W, Abir G, Bianco Y, He Z, Desai M, Mathew R, Lee G, Ahuja N, Lyell D, Gibbs R, Aziz N. Health disparities among pregnant women with sars-cov-2 infection at a university medical center in northern California. Am J Obstet Gynecol 2020. [PMCID: PMC7683952 DOI: 10.1016/j.ajog.2020.08.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
26
|
Sperling M, Sie L, Girsen A, Leonard S, Gibbs R. Recurrent preterm birth in the infection pathway. Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2020.08.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
27
|
Robyns T, Willems R, Van Cleemput J, Jhangiani S, Muzny D, Gibbs R, Lupski JR, Breckpot J, Devriendt K, Corveleyn A. Whole exome sequencing in a large pedigree with DCM identifies a novel mutation in RBM20. Acta Cardiol 2020; 75:748-753. [PMID: 31583969 DOI: 10.1080/00015385.2019.1674490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: Familial dilated cardiomyopathy (DCM) is genetically heterogeneous and is associated with mutations in at least 40 different genes. Apart from TTN encoding the giant protein Titin, none of these genes have an expected diagnostic yield of more than 5% complicating genetic diagnosis. Whole exome sequencing (WES) is a powerful alternative for the identification of the causal gene, however variant interpretation remains challenging. We report on WES in a large family with autosomal dominant DCM complicated by end stage heart failure and non-sustained ventricular arrhythmias in whom no causative mutation was identified using a targeted gene panel including 28 genes.Methods and results: WES was applied on 2 affected cousins. Stringent filtering of the identified genetic variants was performed including population variant frequencies, in silico analysis, orthologous and paralogous conservation. Subsequently Sanger sequencing was performed for 10 potential disease causing variants in order to confirm the presence of the variant and to evaluate co-segregation. Only one variant in exon 9 of the RBM20 gene (c.2714T > A, p.Met950Lys, NM_001334363) showed full co-segregation in the 7 affected family members resulting in a maximum 2-point LOD score of 2.1 and suggesting this as the pathogenic mutation responsible for the phenotype. Recently mutations in RBM20 have been linked to arrhythmogenic dilated cardiomyopathy caused by defective splicing of the giant sarcomere protein titin and abnormal calcium handling.Conclusions: We report the identification of a novel mutation in RBM20 by WES in a large pedigree with DCM.
Collapse
Affiliation(s)
- Tomas Robyns
- Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Rik Willems
- Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Johan Van Cleemput
- Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Shalini Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jeroen Breckpot
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Anniek Corveleyn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
28
|
Sperling M, Sie L, Girsen A, Leonard S, Gibbs R. Risk of recurrent clinical chorioamnionitis in California. Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2020.08.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
29
|
Do S, Miller H, Leonard S, Datoc I, Girsen A, Kappagoda S, Gibbs R, Aziz N. Comparison of lactate and procalcitonin levels in pregnant women with vs without intraamniotic infection during the peripartum period: The serum biomarkers of infection in labor evaluation (SMILE). Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2020.08.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
Sabo A, Murdock D, Dugan S, Meng Q, Gingras MC, Hu J, Muzny D, Gibbs R. Community-based recruitment and exome sequencing indicates high diagnostic yield in adults with intellectual disability. Mol Genet Genomic Med 2020; 8:e1439. [PMID: 32767738 PMCID: PMC7549560 DOI: 10.1002/mgg3.1439] [Citation(s) in RCA: 2] [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: 05/01/2020] [Revised: 06/12/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Establishing a genetic diagnosis for individuals with intellectual disability (ID) benefits patients and their families as it may inform the prognosis, lead to appropriate therapy, and facilitate access to medical and supportive services. Exome sequencing has been successfully applied in a diagnostic setting, but most clinical exome referrals are pediatric patients, with many adults with ID lacking a comprehensive genetic evaluation. METHODS Our unique recruitment strategy involved partnering with service and education providers for individuals with ID. We performed exome sequencing and analysis, and clinical variant interpretation for each recruited family. RESULTS All five families enrolled in the study opted-in for the return of genetic results. In three out of five families exome sequencing analysis identified pathogenic or likely pathogenic variants in KANSL1, TUSC3, and MED13L genes. Families discussed the results and any potential medical follow-up in an appointment with a board certified clinical geneticist. CONCLUSION Our study suggests high yield of exome sequencing as a diagnostic tool in adult patients with ID who have not undergone comprehensive sequencing-based genetic testing. Research studies including an option of return of results through a genetic clinic could help minimize the disparity in exome diagnostic testing between pediatric and adult patients with ID.
Collapse
Affiliation(s)
- Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
31
|
Hanna L, Grover G, Perera A, Chaudhery M, Abdullah A, Singh A, Bicknell C, Modarai B, Hamady M, Gibbs R. Carbon-dioxide versus saline flushing of thoracic aortic stents-grafts to reduce vascular brain infarcts: An observational study. Eur J Vasc Endovasc Surg 2020. [DOI: 10.1016/j.ejvs.2019.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
32
|
Scasta JD, Adams M, Gibbs R, Fleury B. Free-ranging horse management in Australia, New Zealand and the United States: socio-ecological dimensions of a protracted environmental conflict. Rangel J 2020. [DOI: 10.1071/rj19019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Management of free-ranging horses (Equus ferus caballus) is a complex socio-ecological issue in Australia (AU), New Zealand (NZ), and the United States (US). In these countries, horses are the results of colonial introductions and occupy very harsh rangeland environments exerting a grazing disturbance that has generated ecological concerns. Although many social and ecological concerns are similar, each country also has nuances. In 2018, we conducted a field-based comparison of AU, NZ, and US using an inductive approach to identify similarities, differences, and emerging themes through conversations with >100 individuals from New South Wales Australia, the North Island of New Zealand, and the western US. Additional data sources included field observations and archival documents. Consistent emergent themes identified included: strong public emotion, politicization of management, population growth concerns, negative ecological impact concerns, agreement that horses should be treated humanely, disagreement as to what practices were the most humane, interest and scepticism about fertility control, the need for transparency, compromise to accommodating horses and acknowledgement of social values, and recognition that collaboration is the only means to achieve both healthy rangelands and healthy horses. Unique themes identified included: NZ empowering advocate groups to become part of the solution, conflict between horses and livestock is a mostly US conflict, equids originated in the US, concern about the sustainability of adoption programs, different expectations/options for management on private lands, cultural history such as brumby running in AU, permanent branding of horses in the US, litigation as a uniquely US strategy (although a judgement on recent AU litigation is pending), government data accepted to guide removals in NZ but not always in AU or US, and complex heterogeneous land surface ownership patterns makes management difficult in the US. The difficulty of horse management in these countries is attributed to social intricacies rather than biological/ecological gaps of knowledge.
Collapse
|
33
|
Grover G, Davies AH, Rudarakanchana N, Perera A, Hamady M, Gibbs R. Cerebral Embolic Protection to Prevent Brain Inury in Thoracic Aortic Stent-Grafting (TEVAR). Eur J Vasc Endovasc Surg 2019. [DOI: 10.1016/j.ejvs.2019.06.615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
34
|
Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat 2019; 41:487-501. [PMID: 31692161 DOI: 10.1002/humu.23946] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [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: 05/14/2019] [Revised: 10/25/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022]
Abstract
Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.
Collapse
Affiliation(s)
- Kathie J Ngo
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jessica E Rexach
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Lauren E Petty
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Susan Perlman
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Juliana M Valera
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yuanming Mao
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Mamdouh Aker
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Donna Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alexandra B Nelson
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Sharon Hassin-Baer
- Department of Neurology, Chaim Sheba Medical Center, Movement Disorders Institute, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gemma Poke
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Katherine Neas
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Michael D Geschwind
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel H Geschwind
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stanley F Nelson
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Brent L Fogel
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Clinical Neurogenomics Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| |
Collapse
|
35
|
Hanna L, Gibbs R, Fadl A, Kashef E, Riga C, Bicknell C, Jenkins M, Hamady M. AAA 31. Midterm to Long-term Outcomes of Scallop Endografts in the Management of Aortic Disease With Unfavorable Proximal Landing Zone in the Arch. J Vasc Surg 2019. [DOI: 10.1016/j.jvs.2019.08.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
36
|
Tran-Harding K, Shi Q, Gibbs R, Szabunio M, Wang X. Evaluation of Margin Status of a Breast Lumpectomy Specimen: What the Radiologist Should Know. Curr Probl Diagn Radiol 2019; 48:599-604. [DOI: 10.1067/j.cpradiol.2018.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/22/2022]
|
37
|
Bachert SE, Gibbs R, Ginter PS, Stewart RL. Metachronous cellular angiolipomas of the breast. Breast J 2019; 25:1290-1291. [PMID: 31297919 DOI: 10.1111/tbj.13462] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Emily Bachert
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Richard Gibbs
- Department of Radiology, University of Kentucky, Lexington, Kentucky
| | - Paula S Ginter
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Rachel L Stewart
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky.,Markey Cancer Center, Lexington, Kentucky
| |
Collapse
|
38
|
Loomis SJ, Köttgen A, Li M, Tin A, Coresh J, Boerwinkle E, Gibbs R, Muzny D, Pankow J, Selvin E, Duggal P. Rare variants in SLC5A10 are associated with serum 1,5-anhydroglucitol (1,5-AG) in the Atherosclerosis Risk in Communities (ARIC) Study. Sci Rep 2019; 9:5941. [PMID: 30976018 PMCID: PMC6459884 DOI: 10.1038/s41598-019-42202-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 09/12/2018] [Accepted: 03/21/2019] [Indexed: 01/23/2023] Open
Abstract
Serum 1,5-anhydroglucitol (1,5-AG) is an emerging biomarker used to monitor glycemic control in persons with diabetes. We performed whole-exome sequencing, examining the association between rare, coding genetic variants and 1,5-AG among European ancestry (N = 6,589) and African ancestry (N = 2,309) participants without diagnosed diabetes in the Atherosclerosis Risk in Communities (ARIC) Study. Five variants representing 3 independent signals on chromosome 17 in SLC5A10, a glucose transporter not previously known to transport 1,5-AG, were associated with 1,5-AG levels up to 10.38 µg/mL lower per allele (1,5-AG range 3.4–32.8 µg/mL) in the European ancestry sample and validated in the African ancestry sample. Together these variants explained 6% of the variance in 1,5-AG. Two of these variants (rs61741107, p = 8.85E-56; rs148178887, p = 1.13E-36) were rare, nonsynonymous, and predicted to be damaging or deleterious by multiple algorithms. Gene-based SKAT-O analysis supported these results (SLC5A10 p = 5.13E-64 in European ancestry, validated in African ancestry, p = 0.006). Interestingly, these novel variants are not associated with other biomarkers of hyperglycemia or diabetes (p > 0.2). The large effect sizes and protein-altering, multiple independent signals suggest SLC5A10 may code for an important transporter of 1,5-AG in the kidney, with a potential nonglucose-related effect on 1,5-AG, impacting its clinical utility as a diabetes biomarker in this subpopulation.
Collapse
Affiliation(s)
- Stephanie J Loomis
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anna Köttgen
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.,Institute of Genetic Epidemiology, Medical Center and Faculty of Medicine - University of Freiburg, Freiburg, Germany
| | - Man Li
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.,Division of Nephrology and Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Adrienne Tin
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Josef Coresh
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.,Welch Center for Prevention, Epidemiology, & Clinical Research, The Johns Hopkins University, Baltimore, MD, USA
| | - Eric Boerwinkle
- Department of Epidemiology, The University of Texas Health Science Center at Houston School of Public Health at Houston, Houston, TX, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth Selvin
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.,Welch Center for Prevention, Epidemiology, & Clinical Research, The Johns Hopkins University, Baltimore, MD, USA
| | - Priya Duggal
- Department of Epidemiology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
| |
Collapse
|
39
|
Martin G, Patel N, Grant Y, Jenkins M, Gibbs R, Bicknell C. Antihypertensive medication adherence in chronic type B aortic dissection is an important consideration in the management debate. J Vasc Surg 2018; 68:693-699.e2. [DOI: 10.1016/j.jvs.2017.12.063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 12/14/2017] [Indexed: 01/09/2023]
|
40
|
Lin F, Potter S, Ting M, Chandramohan R, Kakkar N, Wang T, Raesz-Martinez R, Scollon S, Bergstrom K, Lopez-Terrada D, Adesina A, Mohila C, Whitehead W, Ramamurthy U, Hilsenbeck S, Wheeler D, Berg S, Chintagumpala M, Eng C, Gibbs R, Roy A, Plon S, Williams Parsons D. TBIO-20. CLINICAL TUMOR WHOLE EXOME SEQUENCING FOR PEDIATRIC NEURO-ONCOLOGY PATIENTS – RESULTS FROM THE BAYLOR ADVANCING SEQUENCING IN CHILDHOOD CANCER CARE (BASIC3) CLINICAL SEQUENCING STUDY. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.708] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Frank Lin
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - Samara Potter
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - Michelle Ting
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | | | | | - Tao Wang
- Baylor College of Medicine, Houston, TX, USA
| | | | - Sarah Scollon
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - Katie Bergstrom
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - Dolores Lopez-Terrada
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - Adekunle Adesina
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - Carrie Mohila
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - William Whitehead
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | | | | | | | - Stacey Berg
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - Murali Chintagumpala
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | | | | | - Angshumoy Roy
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - Sharon Plon
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| | - D Williams Parsons
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Cancer Center, Houston, TX, USA
| |
Collapse
|
41
|
Arays R, Tran-Harding K, Wu J, Yan D, Durbin EB, Marcinkowski EF, McGrath P, Hawthorne K, Romond EH, Chambers MD, Gibbs R, Mathew A. Neglected breast cancer in the Appalachians. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e13023] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Aju Mathew
- University of Kentucky Markey Cancer Center, Lexington, KY
| |
Collapse
|
42
|
Valera JM, Diaz T, Petty LE, Quintáns B, Yáñez Z, Boerwinkle E, Muzny D, Akhmedov D, Berdeaux R, Sobrido MJ, Gibbs R, Lupski JR, Geschwind DH, Perlman S, Below JE, Fogel BL. Prevalence of spinocerebellar ataxia 36 in a US population. Neurol Genet 2017; 3:e174. [PMID: 28761930 PMCID: PMC5515602 DOI: 10.1212/nxg.0000000000000174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/10/2017] [Indexed: 12/12/2022]
Abstract
Objective: To assess the prevalence and clinical features of individuals affected by spinocerebellar ataxia 36 (SCA36) at a large tertiary referral center in the United States. Methods: A total of 577 patients with undiagnosed sporadic or familial cerebellar ataxia comprehensively evaluated at a tertiary referral ataxia center were molecularly evaluated for SCA36. Repeat primed PCR and fragment analysis were used to screen for the presence of a repeat expansion in the NOP56 gene. Results: Fragment analysis of triplet repeat primed PCR products identified a GGCCTG hexanucleotide repeat expansion in intron 1 of NOP56 in 4 index cases. These 4 SCA36-positive families comprised 2 distinct ethnic groups: white (European) (2) and Asian (Japanese [1] and Vietnamese [1]). Individuals affected by SCA36 exhibited typical clinical features with gait ataxia and age at onset ranging between 35 and 50 years. Patients also suffered from ataxic or spastic limbs, altered reflexes, abnormal ocular movement, and cognitive impairment. Conclusions: In a US population, SCA36 was observed to be a rare disorder, accounting for 0.7% (4/577 index cases) of disease in a large undiagnosed ataxia cohort.
Collapse
Affiliation(s)
- Juliana M Valera
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Tatyana Diaz
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Lauren E Petty
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Beatriz Quintáns
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Zuleima Yáñez
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Eric Boerwinkle
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Donna Muzny
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Dmitry Akhmedov
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Rebecca Berdeaux
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Maria J Sobrido
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Richard Gibbs
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - James R Lupski
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Daniel H Geschwind
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Susan Perlman
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Jennifer E Below
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| | - Brent L Fogel
- Program in Neurogenetics (J.M.V., T.D., D.H.G., S.P., B.L.F.), Department of Neurology and Department of Human Genetics (D.H.G., B.L.F.), David Geffen School of Medicine, University of California Los Angeles; The Human Genetics Center (L.E.P., J.E.B.), University of Texas School of Public Health, Houston; Fundación Pública Galega de Medicina Xenómica-SERGAS (B.Q., Z.Y., M.J.S.), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela; Genomic Medicine Group (U711) (B.Q., Z.Y., M.J.S.), Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain; Grupo del Investigación en Genética (Z.Y.), Universidad Simón Bolívar, Barranquilla, Colombia; Department of Molecular and Human Genetics (E.B., D.M., R.G., J.R.L.) and Human Genome Center (J.R.L.), Baylor College of Medicine, Houston, TX; and Department of Integrative Biology and Pharmacology (D.A., R.B.), Institute of Molecular Medicine Center for Metabolic and Degenerative Diseases (R.B.), and Cell and Regulatory Biology Program of The University of Texas Graduate School of Biomedical Sciences (R.B.), McGovern Medical School at The University of Texas Health Science Center at Houston
| |
Collapse
|
43
|
Zagurovskaya M, Tran-Harding K, Gibbs R. Primary lung carcinoid metastatic to the breast. Radiol Case Rep 2017; 12:223-228. [PMID: 28491156 PMCID: PMC5417764 DOI: 10.1016/j.radcr.2017.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 11/24/2016] [Revised: 01/28/2017] [Accepted: 02/05/2017] [Indexed: 01/29/2023] Open
Abstract
Lung carcinoid tumors account for approximately 2% of lung cancers, with 10% of the tumors represented by the atypical type. While atypical carcinoids are metastatic to intrathoracic lymph nodes in approximately half of the cases on the initial presentation, distant metastases are seen in only 20% of the patients and are found most frequently in bones, liver, adrenal glands, and brain. We present a case of an unusual metastatic disease to the breast in 51-year-old female who developed a new breast mass 2 years after left lower lobectomy due to atypical carcinoid tumor. Atypical pulmonary carcinoid metastases to the breast are exceptionally uncommon, yet they are important considerations for appropriate management, especially with an anamnesis of this neoplasm.
Collapse
Affiliation(s)
- Marianna Zagurovskaya
- Department of Diagnostic Radiology, University of Kentucky Chandler Medical Center, 800 Rose St. HX315E, Lexington, KY, USA
| | - Karen Tran-Harding
- Department of Diagnostic Radiology, University of Kentucky Chandler Medical Center, 800 Rose St. HX315E, Lexington, KY, USA
| | - Richard Gibbs
- Department of Diagnostic Radiology, University of Kentucky Chandler Medical Center, 800 Rose St. HX315E, Lexington, KY, USA
| |
Collapse
|
44
|
Chen Y, Zhao L, Wang Y, Cao M, Gelowani V, Xu M, Agrawal SA, Li Y, Daiger SP, Gibbs R, Wang F, Chen R. SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. BMC Bioinformatics 2017; 18:147. [PMID: 28253855 PMCID: PMC5335817 DOI: 10.1186/s12859-017-1566-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 04/16/2016] [Accepted: 02/24/2017] [Indexed: 12/15/2022] Open
Abstract
Background Targeted next-generation sequencing (NGS) has been widely used as a cost-effective way to identify the genetic basis of human disorders. Copy number variations (CNVs) contribute significantly to human genomic variability, some of which can lead to disease. However, effective detection of CNVs from targeted capture sequencing data remains challenging. Results Here we present SeqCNV, a novel CNV calling method designed to use capture NGS data. SeqCNV extracts the read depth information and utilizes the maximum penalized likelihood estimation (MPLE) model to identify the copy number ratio and CNV boundary. We applied SeqCNV to both bacterial artificial clone (BAC) and human patient NGS data to identify CNVs. These CNVs were validated by array comparative genomic hybridization (aCGH). Conclusions SeqCNV is able to robustly identify CNVs of different size using capture NGS data. Compared with other CNV-calling methods, SeqCNV shows a significant improvement in both sensitivity and specificity. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1566-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yong Chen
- Shanghai Key Lab of Intelligent Information Processing, Shanghai, China.,School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Li Zhao
- Structural and Computational Biology & Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yi Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Ming Cao
- University of Texas Health Science Center, Houston, TX, USA
| | - Violet Gelowani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Smriti A Agrawal
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stephen P Daiger
- Department of Ophthalmology and Visual Sciences, University of Texas Health Science Center, Houston, TX, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Fei Wang
- Shanghai Key Lab of Intelligent Information Processing, Shanghai, China. .,School of Computer Science and Technology, Fudan University, Shanghai, China.
| | - Rui Chen
- Structural and Computational Biology & Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
45
|
Morrison AC, Huang Z, Yu B, Metcalf G, Liu X, Ballantyne C, Coresh J, Yu F, Muzny D, Feofanova E, Rustagi N, Gibbs R, Boerwinkle E. Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits. Am J Hum Genet 2017; 100:205-215. [PMID: 28089252 DOI: 10.1016/j.ajhg.2016.12.009] [Citation(s) in RCA: 42] [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: 08/24/2016] [Accepted: 12/14/2016] [Indexed: 01/11/2023] Open
Abstract
Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes. These tests were performed treating all variants equally as well as with individual variants weighted by a measure of predicted functional consequence. Significant findings were assessed in 1,705 individuals of European ancestry. After these steps, we identified and replicated components of the genomic landscape significantly associated with heart- and blood-related traits. For two traits, lipoprotein(a) levels and neutrophil count, aggregate tests of low-frequency and rare variation were significantly associated across multiple motifs. For a third trait, cardiac troponin T, investigation of regulatory domains identified a locus on chromosome 9. These practical approaches for WGS analysis led to the identification of informative genomic regions and also showed that defined non-coding regions, such as first introns of genes and regulatory domains, are associated with important risk factor phenotypes. This study illustrates the tractable nature of WGS data and outlines an approach for characterizing the genetic architecture of complex traits.
Collapse
Affiliation(s)
- Alanna C Morrison
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA.
| | - Zhuoyi Huang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bing Yu
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaoming Liu
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Christie Ballantyne
- Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX 77030, USA; Houston Methodist Debakey Heart and Vascular Center, Houston, TX 77030, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elena Feofanova
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Navin Rustagi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
46
|
Machol K, Jain M, Almannai M, Orand T, Lu JT, Tran A, Chen Y, Schlesinger A, Gibbs R, Bonafe L, Campos-Xavier AB, Unger S, Superti-Furga A, Lee BH, Campeau PM, Burrage LC. Corner fracture type spondylometaphyseal dysplasia: Overlap with type II collagenopathies. Am J Med Genet A 2016; 173:733-739. [PMID: 27888646 DOI: 10.1002/ajmg.a.38059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 09/01/2016] [Accepted: 10/27/2016] [Indexed: 01/04/2023]
Abstract
Spondylometaphyseal dysplasia (SMD) corner fracture type (also known as SMD "Sutcliffe" type, MIM 184255) is a rare skeletal dysplasia that presents with mild to moderate short stature, developmental coxa vara, mild platyspondyly, corner fracture-like lesions, and metaphyseal abnormalities with sparing of the epiphyses. The molecular basis for this disorder has yet to be clarified. We describe two patients with SMD corner fracture type and heterozygous pathogenic variants in COL2A1. These two cases together with a third case of SMD corner fracture type with a heterozygous COL2A1 pathogenic variant previously described suggest that this disorder overlaps with type II collagenopathies. The finding of one of the pathogenic variants in a previously reported case of spondyloepimetaphyseal dysplasia (SEMD) Strudwick type and the significant clinical similarity suggest an overlap between SMD corner fracture and SEMD Strudwick types. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Keren Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mahim Jain
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mohammed Almannai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Thibault Orand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - James T Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alyssa Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yuqing Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alan Schlesinger
- Department of Pediatric Radiology, Texas Children's Hospital, Houston, Texas
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Luisa Bonafe
- Centre for Molecular Diseases and Department of Pediatrics, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland
| | - Ana Belinda Campos-Xavier
- Centre for Molecular Diseases and Department of Pediatrics, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland
| | - Sheila Unger
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Andrea Superti-Furga
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Brendan H Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
47
|
Grover G, Perera A, Rudarakanchana N, Hamady M, Gibbs R. TCT-806 Neuroprotection in thoracic aortic stent-grafting; use of a cerberal embolic protection device. J Am Coll Cardiol 2016. [DOI: 10.1016/j.jacc.2016.09.837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
48
|
Huang Z, Rustagi N, Veeraraghavan N, Carroll A, Gibbs R, Boerwinkle E, Venkata MG, Yu F. A hybrid computational strategy to address WGS variant analysis in >5000 samples. BMC Bioinformatics 2016; 17:361. [PMID: 27612449 PMCID: PMC5018196 DOI: 10.1186/s12859-016-1211-6] [Citation(s) in RCA: 4] [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: 02/24/2016] [Accepted: 08/25/2016] [Indexed: 11/22/2022] Open
Abstract
Background The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies. Results We present a high throughput framework including multiple variant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastructure consisting of cloud AWS, supercomputers and local high performance computing infrastructures. We present a novel binning approach for large scale joint variant calling and imputation which can scale up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity. As a proof of principle, we present results of analysis on Cohorts for Heart And Aging Research in Genomic Epidemiology (CHARGE) WGS freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. The callers used were SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud. We used Amazon AWS, a 4000-core in-house cluster at Baylor College of Medicine, IBM power PC Blue BioU at Rice and Rhea at Oak Ridge National Laboratory (ORNL) for the computation. AWS was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for the imputation and phasing step. All other steps were carried out on the local compute cluster. The entire operation used 5.2 million core hours and only transferred a total of 6 TB of data across the platforms. Conclusions Even with increasing sizes of whole genome datasets, ensemble joint calling of SNVs for low coverage data can be accomplished in a scalable, cost effective and fast manner by using heterogeneous computing platforms without compromising on the quality of variants. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1211-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zhuoyi Huang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Navin Rustagi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | | | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
49
|
Nienaber CA, Clough RE, Sakalihasan N, Suzuki T, Gibbs R, Mussa F, Jenkins MP, Thompson MM, Evangelista A, Yeh JSM, Cheshire N, Rosendahl U, Pepper J. Aortic dissection. Nat Rev Dis Primers 2016; 2:16071. [PMID: 27560366 DOI: 10.1038/nrdp.2016.71] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
50
|
Martin G, Riga C, Gibbs R, Jenkins M, Hamady M, Bicknell C. Short- and Long-term Results of Hybrid Arch and Proximal Descending Thoracic Aortic Repair. J Endovasc Ther 2016; 23:783-90. [DOI: 10.1177/1526602816655446] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Purpose: To evaluate the short- and long-term outcomes of hybrid repair of the arch and proximal descending aorta in a single tertiary center for aortic disease. Methods: A retrospective analysis was performed of 55 patients (median age 67 years; 36 men) who underwent hybrid repair of thoracic aortic pathology with involvement of the arch between January 2005 and May 2015 at a single tertiary center. The pathologies included 40 (73%) with aneurysmal disease, 10 (18%) acute type B aortic dissections, 2 with acute aortic syndrome, an acute type A dissection, and left and aberrant right subclavian artery aneurysms. Seven (13%) procedures were performed as an emergency. Demographics and procedure characteristics were collected for analysis of survival and reinterventions. Results: Complete aortic debranching was performed in 14 (25%) to facilitate endograft placement in zone 0; debranching was partial in 20 (36%) patients for zone 1 deployments and 21 (38%) for zone 2. Primary technical success was achieved in 51 (93%) cases. One patient died in-hospital from aneurysm rupture following aortic debranching prior to stent-graft repair. In another, the stent-graft procedure proved infeasible and was abandoned. The other 2 technical failures were due to type Ia endoleaks. Five (9%) patients died in-hospital (4 of 48 elective and 1 of 7 emergency cases); 2 of these patients died within 30 days (4%). Eight (14%) patients had a stroke, 6 of 48 elective and 2 of the 7 emergency patients. Spinal cord ischemia was reported in 3 (6%) patients. Mean follow-up was 74.6 months. Overall cumulative survival was 70% at 1 year, 68% at 2 years, and 57% at 5 years. Reintervention to the proximal landing zone for type Ia endoleak was required in 6% of cases. The overall rate of aortic reintervention was 18% at 1 year, 21% at 2 years, and 36% at 5 years. Overall extra-anatomic graft patency was 99%. Conclusion: Hybrid repair of the aortic arch and proximal descending thoracic aorta is technically feasible, with acceptable short-term mortality. There is a low rate of proximal landing zone reintervention when hybrid techniques are used to create an adequate proximal landing zone. Extra-anatomic bypass grafts have good long-term patency. Ongoing disease progression means that further distal aortic interventions are often necessary in patients with extensive disease.
Collapse
Affiliation(s)
- Guy Martin
- Department of Surgery and Cancer, Imperial College London, UK
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Celia Riga
- Department of Surgery and Cancer, Imperial College London, UK
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Richard Gibbs
- Department of Surgery and Cancer, Imperial College London, UK
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Michael Jenkins
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| | - Mohamad Hamady
- Department of Surgery and Cancer, Imperial College London, UK
- Department of Interventional Radiology, Imperial College Healthcare NHS Trust, London, UK
| | - Colin Bicknell
- Department of Surgery and Cancer, Imperial College London, UK
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, UK
| |
Collapse
|