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Hecker J, Chun S, Samiei A, Liu C, Laurie C, Kachroo P, Lutz SM, Lee S, Smith AV, Lasky-Su J, Cho MH, Sharma S, Soto Quirós ME, Avila L, Celedón JC, Raby B, Zhou X, Silverman EK, DeMeo DL, Lange C, Weiss ST. FGF20 and PGM2 variants are associated with childhood asthma in family-based whole-genome sequencing studies. Hum Mol Genet 2023; 32:696-707. [PMID: 36255742 PMCID: PMC9896483 DOI: 10.1093/hmg/ddac258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Asthma is a heterogeneous common respiratory disease that remains poorly understood. The established genetic associations fail to explain the high estimated heritability, and the prevalence of asthma differs between populations and geographic regions. Robust association analyses incorporating different genetic ancestries and whole-genome sequencing data may identify novel genetic associations. METHODS We performed family-based genome-wide association analyses of childhood-onset asthma based on whole-genome sequencing (WGS) data for the 'The Genetic Epidemiology of Asthma in Costa Rica' study (GACRS) and the Childhood Asthma Management Program (CAMP). Based on parent-child trios with children diagnosed with asthma, we performed a single variant analysis using an additive and a recessive genetic model and a region-based association analysis of low-frequency and rare variants. RESULTS Based on 1180 asthmatic trios (894 GACRS trios and 286 CAMP trios, a total of 3540 samples with WGS data), we identified three novel genetic loci associated with childhood-onset asthma: rs4832738 on 4p14 ($P=1.72\ast{10}^{-9}$, recessive model), rs1581479 on 8p22 ($P=1.47\ast{10}^{-8}$, additive model) and rs73367537 on 10q26 ($P=1.21\ast{10}^{-8}$, additive model in GACRS only). Integrative analyses suggested potential novel candidate genes underlying these associations: PGM2 on 4p14 and FGF20 on 8p22. CONCLUSION Our family-based whole-genome sequencing analysis identified three novel genetic loci for childhood-onset asthma. Gene expression data and integrative analyses point to PGM2 on 4p14 and FGF20 on 8p22 as linked genes. Furthermore, region-based analyses suggest independent potential low-frequency/rare variant associations on 8p22. Follow-up analyses are needed to understand the functional mechanisms and generalizability of these associations.
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Affiliation(s)
- Julian Hecker
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmad Samiei
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Cuining Liu
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sharon M Lutz
- Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care, Boston, MA 02215, USA
| | - Sanghun Lee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin-si, 16890, South Korea
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, 10101 San José, Costa Rica
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Benjamin Raby
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
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2
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Lee S, Prokopenko D, Kelly RS, Lutz S, Ann Lasky-Su J, Cho MH, Laurie C, Celedón JC, Lange C, Weiss ST, Hecker J, DeMeo DL. Zinc finger protein 33B demonstrates sex interaction with atopy-related markers in childhood asthma. Eur Respir J 2023; 61:2200479. [PMID: 35953101 PMCID: PMC10124713 DOI: 10.1183/13993003.00479-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/14/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Sex differences related to immune responses can influence atopic manifestations in childhood asthma. While genome-wide association studies have investigated a sex-specific genetic architecture of the immune response, gene-by-sex interactions have not been extensively analysed for atopy-related markers including allergy skin tests, IgE and eosinophils in asthmatic children. METHODS We performed a genome-wide gene-by-sex interaction analysis for atopy-related markers using whole-genome sequencing data based on 889 trios from the Genetic Epidemiology of Asthma in Costa Rica Study (GACRS) and 284 trios from the Childhood Asthma Management Program (CAMP). We also tested the findings in UK Biobank participants with self-reported childhood asthma. Furthermore, downstream analyses in GACRS integrated gene expression to disentangle observed associations. RESULTS Single nucleotide polymorphism (SNP) rs1255383 at 10q11.21 demonstrated a genome-wide significant gene-by-sex interaction (pinteraction=9.08×10-10) for atopy (positive skin test) with opposite direction of effects between females and males. In the UK Biobank participants with a history of childhood asthma, the signal was consistently observed with the same sex-specific effect directions for high eosinophil count (pinteraction=0.0058). Gene expression of ZNF33B (zinc finger protein 33B), located at 10q11.21, was moderately associated with atopy in girls, but not in boys. CONCLUSIONS We report SNPs in/near a zinc finger gene as novel sex-differential loci for atopy-related markers with opposite effect directions in females and males. A potential role for ZNF33B should be studied further as an important driver of sex-divergent features of atopy in childhood asthma.
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Affiliation(s)
- Sanghun Lee
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin, South Korea
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- NH Institute for Natural Product Research, Myungji Hospital, Goyang-si, South Korea
| | - Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sharon Lutz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jessica Ann Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
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3
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Laurie C. Development of the advanced physiotherapy practitioner in managing acute orthopaedic injuries previously managed by orthopaedic consultants. Physiotherapy 2021. [DOI: 10.1016/j.physio.2021.10.116] [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: 11/30/2022]
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4
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Lee S, Lasky-Su J, Won S, Laurie C, Celedón JC, Lange C, Weiss S, Hecker J. Novel recessive locus for body mass index in childhood asthma. Thorax 2021; 76:1227-1230. [PMID: 33888571 PMCID: PMC8531156 DOI: 10.1136/thoraxjnl-2020-215742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/16/2020] [Accepted: 03/16/2021] [Indexed: 11/03/2022]
Abstract
Most genome-wide association studies of obesity and body mass index (BMI) have so far assumed an additive mode of inheritance in their analysis, although association testing supports a recessive effect for some of the established loci, for example, rs1421085 in FTO In two whole-genome sequencing (WGS) studies of children with asthma and their parents (892 Costa Rican trios and 286 North American trios), we discovered an association between a locus (rs9292139) in LOC102724122 and BMI that reaches genome-wide significance under a recessive model in the combined analysis. As the association does not achieve significance under an additive model, our finding illustrates the benefits of the recessive model in WGS analyses.
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Affiliation(s)
- Sanghun Lee
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University-Jukjeon Campus, Yongin, South Korea
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sungho Won
- Department of Public Health Science, Seoul National University, Gwanak-gu, South Korea
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Juan Carlos Celedón
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Scott Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
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5
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Hecker J, Townes FW, Kachroo P, Laurie C, Lasky-Su J, Ziniti J, Cho MH, Weiss ST, Laird NM, Lange C. A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests. Bioinformatics 2021; 36:5432-5438. [PMID: 33367522 PMCID: PMC8016468 DOI: 10.1093/bioinformatics/btaa1055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/20/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Analysis of rare variants in family-based studies remains a challenge. Transmission-based approaches provide robustness against population stratification, but the evaluation of the significance of test statistics based on asymptotic theory can be imprecise. Also, power will depend heavily on the choice of the test statistic and on the underlying genetic architecture of the locus, which will be generally unknown. RESULTS In our proposed framework, we utilize the FBAT haplotype algorithm to obtain the conditional offspring genotype distribution under the null hypothesis given the sufficient statistic. Based on this conditional offspring genotype distribution, the significance of virtually any association test statistic can be evaluated based on simulations or exact computations, without the need for asymptotic approximations. Besides standard linear burden-type statistics, this enables our approach to also evaluate other test statistics such as variance components statistics, higher criticism approaches, and maximum-single-variant-statistics, where asymptotic theory might be involved or does not provide accurate approximations for rare variant data. Based on these P-values, combined test statistics such as the aggregated Cauchy association test (ACAT) can also be utilized. In simulation studies, we show that our framework outperforms existing approaches for family-based studies in several scenarios. We also applied our methodology to a TOPMed whole-genome sequencing dataset with 897 asthmatic trios from Costa Rica. AVAILABILITY AND IMPLEMENTATION FBAT software is available at https://sites.google.com/view/fbatwebpage. Simulation code is available at https://github.com/julianhecker/FBAT_rare_variant_test_simulations. Whole-genome sequencing data for 'NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica' is available at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000988.v4.p1. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Julian Hecker
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - F William Townes
- Department of Computer Science, Princeton University, Princeton, NJ 08540-5233, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195-1617, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - John Ziniti
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nan M Laird
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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6
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Bick AG, Weinstock JS, Nandakumar SK, Fulco CP, Bao EL, Zekavat SM, Szeto MD, Liao X, Leventhal MJ, Nasser J, Chang K, Laurie C, Burugula BB, Gibson CJ, Niroula A, Lin AE, Taub MA, Aguet F, Ardlie K, Mitchell BD, Barnes KC, Moscati A, Fornage M, Redline S, Psaty BM, Silverman EK, Weiss ST, Palmer ND, Vasan RS, Burchard EG, Kardia SLR, He J, Kaplan RC, Smith NL, Arnett DK, Schwartz DA, Correa A, de Andrade M, Guo X, Konkle BA, Custer B, Peralta JM, Gui H, Meyers DA, McGarvey ST, Chen IYD, Shoemaker MB, Peyser PA, Broome JG, Gogarten SM, Wang FF, Wong Q, Montasser ME, Daya M, Kenny EE, North KE, Launer LJ, Cade BE, Bis JC, Cho MH, Lasky-Su J, Bowden DW, Cupples LA, Mak ACY, Becker LC, Smith JA, Kelly TN, Aslibekyan S, Heckbert SR, Tiwari HK, Yang IV, Heit JA, Lubitz SA, Johnsen JM, Curran JE, Wenzel SE, Weeks DE, Rao DC, Darbar D, Moon JY, Tracy RP, Buth EJ, Rafaels N, Loos RJF, Durda P, Liu Y, Hou L, Lee J, Kachroo P, Freedman BI, Levy D, Bielak LF, Hixson JE, Floyd JS, Whitsel EA, Ellinor PT, Irvin MR, Fingerlin TE, Raffield LM, Armasu SM, Wheeler MM, Sabino EC, Blangero J, Williams LK, Levy BD, Sheu WHH, Roden DM, Boerwinkle E, Manson JE, Mathias RA, Desai P, Taylor KD, Johnson AD, Auer PL, Kooperberg C, Laurie CC, Blackwell TW, Smith AV, Zhao H, Lange E, Lange L, Rich SS, Rotter JI, Wilson JG, Scheet P, Kitzman JO, Lander ES, Engreitz JM, Ebert BL, Reiner AP, Jaiswal S, Abecasis G, Sankaran VG, Kathiresan S, Natarajan P. Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes. Nature 2021; 591:E27. [PMID: 33707633 DOI: 10.1038/s41586-021-03280-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexander G Bick
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Satish K Nandakumar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Erik L Bao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Seyedeh M Zekavat
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Mindy D Szeto
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiaotian Liao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyle Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | | | - Abhishek Niroula
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy E Lin
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 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
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Colorado Center for Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Arden Moscati
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.,Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susan Redline
- Harvard Medical School, Boston, MA, USA.,Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 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 Services, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Edwin K Silverman
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott T Weiss
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ramachandran S Vasan
- Departments of Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, USA
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.,Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA.,Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA.,Seattle Epidemiologic Information and Research Center, Department of Veterans Affairs, Office of Research and Development, Seattle, WA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | | | - Adolfo Correa
- Departments of Medicine and Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Barbara A Konkle
- Bloodworks Northwest, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, University of Arizona, Tucson, AZ, USA
| | - Stephen T McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Ida Yii-Der Chen
- Medical Genetics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - M Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Fei Fei Wang
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - May E Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography, and Biometry, Intramural Research Program, National Institute on Aging, Bethesda, MD, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael H Cho
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jessica Lasky-Su
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - L Adrienne Cupples
- Departments of Biostatistics and Epidemiology, 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
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.,Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ivana V Yang
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - John A Heit
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Steven A Lubitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jill M Johnsen
- Bloodworks Northwest, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel E Weeks
- Departments of Human Genetics and Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Erin J Buth
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Priyadarshini Kachroo
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA, USA.,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James E Hixson
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Patrick T Ellinor
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tasha E Fingerlin
- Center for Genes Environment and Health, National Jewish Health, Denver, CO, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | | | - Marsha M Wheeler
- Department of Genome Science, University of Washington, Seattle, WA, USA
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Bruce D Levy
- Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wayne Huey-Herng Sheu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - JoAnn E Manson
- Harvard Medical School, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Pinkal Desai
- Department of Medicine, Weill Cornell Medical School, New York, NY, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA.,Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Andrew D Johnson
- Framingham Heart Study, Framingham, MA, USA.,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of WisconsinMilwaukee, Milwaukee, WI, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Albert V Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Hongyu Zhao
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA.,Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Ethan Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA.,Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Department of Biology, MIT, Cambridge, MA, USA
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Howard Hughes Medical Institute, 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
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gonçalo Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Verve Therapeutics, Cambridge, MA, USA.
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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7
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Lee S, Lasky-Su JA, Lange C, Kim W, Kumar PL, McDonald MLN, Vaz Fragoso CA, Laurie C, Raby BA, Celedón JC, Cho MH, Won S, Weiss ST, Hecker J. A novel locus for exertional dyspnoea in childhood asthma. Eur Respir J 2021; 57:13993003.01224-2020. [PMID: 32855217 DOI: 10.1183/13993003.01224-2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022]
Abstract
Most children diagnosed with asthma have respiratory symptoms such as cough, dyspnoea and wheezing, which are also important markers of overall respiratory function. A decade of genome-wide association studies (GWAS) have investigated genetic susceptibility to asthma itself, but few have focused on important respiratory symptoms that characterise childhood asthma.Using whole-genome sequencing (WGS) data for 894 asthmatic trios from a Costa Rican cohort, we performed family-based association tests (FBATs) to assess the association between genetic variants and multiple asthma-relevant respiratory phenotypes: cough, phlegm, wheezing, exertional dyspnoea and exertional chest tightness. We tested whether genome-wide significant associations were replicated in two additional studies: 1) 286 asthmatic trios from the Childhood Asthma Management Program (CAMP), and 2) 2691 African American current or former smokers from the COPDGene study.In the 894 Costa Rican trios, we identified a genome-wide significant association (p=2.16×10-9) between exertional dyspnoea and the single nucleotide polymorphism (SNP) rs10165869, located on chromosome 2q37.3, that was replicated in the CAMP cohort (p=0.023) with the same direction of association (combined p=3.28×10-10). This association was not found in the African American participants from COPDGene. We also found suggestive evidence for an association between SNP rs10165869 and the atypical chemokine receptor 3 (ACKR3).Our finding encourages the secondary association analysis of a wider range of phenotypes that characterise respiratory symptoms in other airway diseases/studies.
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Affiliation(s)
- Sanghun Lee
- Dept of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin, South Korea.,Dept of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jessica Ann Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Christoph Lange
- Dept of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Preeti Lakshman Kumar
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Merry-Lynn N McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Cecelia Laurie
- Dept of Biostatistics, University of Washington, Seattle, WA, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sungho Won
- Dept of Public Health Science, Seoul National University, Seoul, South Korea
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
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8
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Lee S, Lasky-Su J, Kim W, Won S, Laurie C, Celedón JC, Lange C, Weiss ST, Hecker J. An interaction of the 17q12-21 locus with mold exposure in childhood asthma. Pediatr Allergy Immunol 2021; 32:373-376. [PMID: 32946604 PMCID: PMC8277824 DOI: 10.1111/pai.13376] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Sanghun Lee
- Department of Medical Consilience, Division of Medicine, Graduate school, Dankook University, Yongin, South Korea.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sungho Won
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Public Health Science, Seoul National University, Seoul, South Korea
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
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9
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Honigberg MC, Zekavat SM, Niroula A, Griffin GK, Bick AG, Pirruccello JP, Nakao T, Whitsel EA, Farland LV, Laurie C, Kooperberg C, Manson JE, Gabriel S, Libby P, Reiner AP, Ebert BL, Natarajan P. Premature Menopause, Clonal Hematopoiesis, and Coronary Artery Disease in Postmenopausal Women. Circulation 2020; 143:410-423. [PMID: 33161765 DOI: 10.1161/circulationaha.120.051775] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Premature menopause is an independent risk factor for cardiovascular disease in women, but mechanisms underlying this association remain unclear. Clonal hematopoiesis of indeterminate potential (CHIP), the age-related expansion of hematopoietic cells with leukemogenic mutations without detectable malignancy, is associated with accelerated atherosclerosis. Whether premature menopause is associated with CHIP is unknown. METHODS We included postmenopausal women from the UK Biobank (n=11 495) aged 40 to 70 years with whole exome sequences and from the Women's Health Initiative (n=8111) aged 50 to 79 years with whole genome sequences. Premature menopause was defined as natural or surgical menopause occurring before age 40 years. Co-primary outcomes were the presence of any CHIP and CHIP with variant allele frequency >0.1. Logistic regression tested the association of premature menopause with CHIP, adjusted for age, race, the first 10 principal components of ancestry, smoking, diabetes, and hormone therapy use. Secondary analyses considered natural versus surgical premature menopause and gene-specific CHIP subtypes. Multivariable-adjusted Cox models tested the association between CHIP and incident coronary artery disease. RESULTS The sample included 19 606 women, including 418 (2.1%) with natural premature menopause and 887 (4.5%) with surgical premature menopause. Across cohorts, CHIP prevalence in postmenopausal women with versus without a history of premature menopause was 8.8% versus 5.5% (P<0.001), respectively. After multivariable adjustment, premature menopause was independently associated with CHIP (all CHIP: odds ratio, 1.36 [95% 1.10-1.68]; P=0.004; CHIP with variant allele frequency >0.1: odds ratio, 1.40 [95% CI, 1.10-1.79]; P=0.007). Associations were larger for natural premature menopause (all CHIP: odds ratio, 1.73 [95% CI, 1.23-2.44]; P=0.001; CHIP with variant allele frequency >0.1: odds ratio, 1.91 [95% CI, 1.30-2.80]; P<0.001) but smaller and nonsignificant for surgical premature menopause. In gene-specific analyses, only DNMT3A CHIP was significantly associated with premature menopause. Among postmenopausal middle-aged women, CHIP was independently associated with incident coronary artery disease (hazard ratio associated with all CHIP: 1.36 [95% CI, 1.07-1.73]; P=0.012; hazard ratio associated with CHIP with variant allele frequency >0.1: 1.48 [95% CI, 1.13-1.94]; P=0.005). CONCLUSIONS Premature menopause, especially natural premature menopause, is independently associated with CHIP among postmenopausal women. Natural premature menopause may serve as a risk signal for predilection to develop CHIP and CHIP-associated cardiovascular disease.
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Affiliation(s)
- Michael C Honigberg
- Cardiology Division (M.C.H., J.P.P., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Department of Medicine (M.C.H., J.P.P., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Cardiovascular Research Center and Center for Genomic Medicine (M.C.H., J.P.P., T.N., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.)
| | - Seyedeh M Zekavat
- Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.).,Yale University School of Medicine, New Haven, CT (S.M.Z.)
| | - Abhishek Niroula
- Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.).,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA (A.N., T.N., B.L.E.)
| | - Gabriel K Griffin
- Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.).,Department of Pathology (G.K.G., T.N.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Alexander G Bick
- Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.).,Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN (A.G.B.)
| | - James P Pirruccello
- Cardiology Division (M.C.H., J.P.P., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Department of Medicine (M.C.H., J.P.P., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Cardiovascular Research Center and Center for Genomic Medicine (M.C.H., J.P.P., T.N., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.)
| | - Tetsushi Nakao
- Cardiovascular Research Center and Center for Genomic Medicine (M.C.H., J.P.P., T.N., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.).,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA (A.N., T.N., B.L.E.).,Department of Pathology (G.K.G., T.N.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Eric A Whitsel
- Gillings School of Global Public Health and School of Medicine, University of Chapel Hill, NC (E.A.W.)
| | - Leslie V Farland
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson (L.V.F.)
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle (C.L.)
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (C.K., A.P.R.)
| | - JoAnn E Manson
- Division of Preventive Medicine (J.E.M.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (J.E.M.)
| | - Stacey Gabriel
- Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.)
| | - Peter Libby
- Cardiovascular Division, Brigham and Women's Hospital Heart & Vascular Center, Boston, MA (P.L.)
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (C.K., A.P.R.)
| | - Benjamin L Ebert
- Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.).,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA (A.N., T.N., B.L.E.)
| | | | - Pradeep Natarajan
- Cardiology Division (M.C.H., J.P.P., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Department of Medicine (M.C.H., J.P.P., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Cardiovascular Research Center and Center for Genomic Medicine (M.C.H., J.P.P., T.N., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston.,Broad Institute of Harvard and MIT, Cambridge, MA (M.C.H., S.M.Z., A.N., G.K.G., A.G.B., J.P.P., T.N., S.G., B.L.E., P.N.)
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10
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Bick AG, Weinstock JS, Nandakumar SK, Fulco CP, Bao EL, Zekavat SM, Szeto MD, Liao X, Leventhal MJ, Nasser J, Chang K, Laurie C, Burugula BB, Gibson CJ, Lin AE, Taub MA, Aguet F, Ardlie K, Mitchell BD, Barnes KC, Moscati A, Fornage M, Redline S, Psaty BM, Silverman EK, Weiss ST, Palmer ND, Vasan RS, Burchard EG, Kardia SLR, He J, Kaplan RC, Smith NL, Arnett DK, Schwartz DA, Correa A, de Andrade M, Guo X, Konkle BA, Custer B, Peralta JM, Gui H, Meyers DA, McGarvey ST, Chen IYD, Shoemaker MB, Peyser PA, Broome JG, Gogarten SM, Wang FF, Wong Q, Montasser ME, Daya M, Kenny EE, North KE, Launer LJ, Cade BE, Bis JC, Cho MH, Lasky-Su J, Bowden DW, Cupples LA, Mak ACY, Becker LC, Smith JA, Kelly TN, Aslibekyan S, Heckbert SR, Tiwari HK, Yang IV, Heit JA, Lubitz SA, Johnsen JM, Curran JE, Wenzel SE, Weeks DE, Rao DC, Darbar D, Moon JY, Tracy RP, Buth EJ, Rafaels N, Loos RJF, Durda P, Liu Y, Hou L, Lee J, Kachroo P, Freedman BI, Levy D, Bielak LF, Hixson JE, Floyd JS, Whitsel EA, Ellinor PT, Irvin MR, Fingerlin TE, Raffield LM, Armasu SM, Wheeler MM, Sabino EC, Blangero J, Williams LK, Levy BD, Sheu WHH, Roden DM, Boerwinkle E, Manson JE, Mathias RA, Desai P, Taylor KD, Johnson AD, Auer PL, Kooperberg C, Laurie CC, Blackwell TW, Smith AV, Zhao H, Lange E, Lange L, Rich SS, Rotter JI, Wilson JG, Scheet P, Kitzman JO, Lander ES, Engreitz JM, Ebert BL, Reiner AP, Jaiswal S, Abecasis G, Sankaran VG, Kathiresan S, Natarajan P. Inherited causes of clonal haematopoiesis in 97,691 whole genomes. Nature 2020; 586:763-768. [PMID: 33057201 PMCID: PMC7944936 DOI: 10.1038/s41586-020-2819-2] [Citation(s) in RCA: 323] [Impact Index Per Article: 80.8] [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: 09/25/2019] [Accepted: 07/03/2020] [Indexed: 12/17/2022]
Abstract
Age is the dominant risk factor for most chronic human diseases; yet the mechanisms by which aging confers this risk are largely unknown.1 Recently, the age-related acquisition of somatic mutations in regenerating hematopoietic stem cell populations leading to clonal expansion was associated with both hematologic cancer 2–4 and coronary heart disease5, a phenomenon termed ‘Clonal Hematopoiesis of Indeterminate Potential’ (CHIP).6 Simultaneous germline and somatic whole genome sequence analysis now provides the opportunity to identify root causes of CHIP. Here, we analyze high-coverage whole genome sequences from 97,691 participants of diverse ancestries in the NHLBI TOPMed program and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid, and inflammatory traits specific to different CHIP genes. Association of a genome-wide set of germline genetic variants identified three genetic loci associated with CHIP status, including one locus at TET2 that was African ancestry specific. In silico-informed in vitro evaluation of the TET2 germline locus identified a causal variant that disrupts a TET2 distal enhancer resulting in increased hematopoietic stem cell self-renewal. Overall, we observe that germline genetic variation shapes hematopoietic stem cell function leading to CHIP through mechanisms that are both specific to clonal hematopoiesis and shared mechanisms leading to somatic mutations across tissues.
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Affiliation(s)
- Alexander G Bick
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Satish K Nandakumar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Erik L Bao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Seyedeh M Zekavat
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Mindy D Szeto
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiaotian Liao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyle Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | | | - Amy E Lin
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 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
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Colorado Center for Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Arden Moscati
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.,Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susan Redline
- Harvard Medical School, Boston, MA, USA.,Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 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 Services, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Edwin K Silverman
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott T Weiss
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ramachandran S Vasan
- Departments of Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, USA
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.,Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA.,Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA.,Seattle Epidemiologic Information and Research Center, Department of Veterans Affairs, Office of Research and Development, Seattle, WA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | | | - Adolfo Correa
- Departments of Medicine and Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Barbara A Konkle
- Bloodworks Northwest, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, University of Arizona, Tucson, AZ, USA
| | - Stephen T McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Ida Yii-Der Chen
- Medical Genetics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - M Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Fei Fei Wang
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - May E Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography, and Biometry, Intramural Research Program, National Institute on Aging, Bethesda, MD, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael H Cho
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jessica Lasky-Su
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - L Adrienne Cupples
- Departments of Biostatistics and Epidemiology, 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
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.,Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ivana V Yang
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - John A Heit
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Steven A Lubitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jill M Johnsen
- Bloodworks Northwest, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel E Weeks
- Departments of Human Genetics and Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Erin J Buth
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Priyadarshini Kachroo
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA, USA.,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James E Hixson
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Patrick T Ellinor
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tasha E Fingerlin
- Center for Genes Environment and Health, National Jewish Health, Denver, CO, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | | | - Marsha M Wheeler
- Department of Genome Science, University of Washington, Seattle, WA, USA
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Bruce D Levy
- Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wayne Huey-Herng Sheu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric Boerwinkle
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - JoAnn E Manson
- Harvard Medical School, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Pinkal Desai
- Department of Medicine, Weill Cornell Medical School, New York, NY, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA.,Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Andrew D Johnson
- Framingham Heart Study, Framingham, MA, USA.,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Albert V Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Hongyu Zhao
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA.,Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Ethan Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA.,Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Department of Biology, MIT, Cambridge, MA, USA
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Howard Hughes Medical Institute, 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
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gonçalo Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sekar Kathiresan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Verve Therapeutics, Cambridge, MA, USA.
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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11
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Raffield LM, Iyengar AK, Wang B, Gaynor SM, Spracklen CN, Zhong X, Kowalski MH, Salimi S, Polfus LM, Benjamin EJ, Bis JC, Bowler R, Cade BE, Choi WJ, Comellas AP, Correa A, Cruz P, Doddapaneni H, Durda P, Gogarten SM, Jain D, Kim RW, Kral BG, Lange LA, Larson MG, Laurie C, Lee J, Lee S, Lewis JP, Metcalf GA, Mitchell BD, Momin Z, Muzny DM, Pankratz N, Park CJ, Rich SS, Rotter JI, Ryan K, Seo D, Tracy RP, Viaud-Martinez KA, Yanek LR, Zhao LP, Lin X, Li B, Li Y, Dupuis J, Reiner AP, Mohlke KL, Auer PL. Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts. Am J Hum Genet 2020; 106:112-120. [PMID: 31883642 PMCID: PMC7042494 DOI: 10.1016/j.ajhg.2019.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 10/04/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequencing (WGS) can improve assessment of low-frequency and rare variants, particularly in non-European populations that have been underrepresented in existing genomic studies. The genetic determinants of C-reactive protein (CRP), a biomarker of chronic inflammation, have been extensively studied, with existing genome-wide association studies (GWASs) conducted in >200,000 individuals of European ancestry. In order to discover novel loci associated with CRP levels, we examined a multi-ancestry population (n = 23,279) with WGS (∼38× coverage) from the Trans-Omics for Precision Medicine (TOPMed) program. We found evidence for eight distinct associations at the CRP locus, including two variants that have not been identified previously (rs11265259 and rs181704186), both of which are non-coding and more common in individuals of African ancestry (∼10% and ∼1% minor allele frequency, respectively, and rare or monomorphic in 1000 Genomes populations of East Asian, South Asian, and European ancestry). We show that the minor (G) allele of rs181704186 is associated with lower CRP levels and decreased transcriptional activity and protein binding in vitro, providing a plausible molecular mechanism for this African ancestry-specific signal. The individuals homozygous for rs181704186-G have a mean CRP level of 0.23 mg/L, in contrast to individuals heterozygous for rs181704186 with mean CRP of 2.97 mg/L and major allele homozygotes with mean CRP of 4.11 mg/L. This study demonstrates the utility of WGS in multi-ethnic populations to drive discovery of complex trait associations of large effect and to identify functional alleles in noncoding regulatory regions.
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Affiliation(s)
- Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Apoorva K Iyengar
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Biqi Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Madeline H Kowalski
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Shabnam Salimi
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Linda M Polfus
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Emelia J Benjamin
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Joshua C Bis
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
| | - Russell Bowler
- Department of Medicine, Division of Pulmonary, Critical Care & Sleep Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Brian E Cade
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alejandro P Comellas
- Department of Medicine, Division of Pulmonary and Critical Care, University of Iowa, Iowa City, IA 52242, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Pedro Cruz
- Illumina Laboratory Services, Illumina Inc., San Diego, CA 92122, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA
| | | | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | | | - Brian G Kral
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Martin G Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jiwon Lee
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Russell P Tracy
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA; Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA
| | | | - Lisa R Yanek
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lue Ping Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53205, USA.
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12
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Choi SH, Lu-Chen W, Roselli C, Lin H, Haggerty CM, Shoemaker MB, Barnard J, Arking DE, Chasman DI, Albert CM, Chaffin M, Tucker NR, Smith JD, Gupta N, Gabriel S, Margolin L, Shea MA, Shaffer CM, Yoneda ZT, Boerwinkle E, Smith NL, Silverman EK, Redline S, Vasan RS, Burchard EG, Gogarten SM, Laurie C, Blackwell TW, Abecasis G, Carey DJ, Fornwalt BK, Smelser DT, Baras A, Dewey FE, Jaquish CE, Papanicolaou GJ, Sotoodehnia N, Van Wagoner DR, Psaty BM, Kathiresan S, Darbar D, Alonso A, Heckbert SR, Chung MK, Roden DM, Benjamin EJ, Murray MF, Lunetta KL, Lubitz SA, Ellinor PT. Association Between Titin Loss-of-Function Variants and Early-Onset Atrial Fibrillation. JAMA 2018; 320:2354-2364. [PMID: 30535219 PMCID: PMC6436530 DOI: 10.1001/jama.2018.18179] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
IMPORTANCE Atrial fibrillation (AF) is the most common arrhythmia affecting 1% of the population. Young individuals with AF have a strong genetic association with the disease, but the mechanisms remain incompletely understood. OBJECTIVE To perform large-scale whole-genome sequencing to identify genetic variants related to AF. DESIGN, SETTING, AND PARTICIPANTS The National Heart, Lung, and Blood Institute's Trans-Omics for Precision Medicine Program includes longitudinal and cohort studies that underwent high-depth whole-genome sequencing between 2014 and 2017 in 18 526 individuals from the United States, Mexico, Puerto Rico, Costa Rica, Barbados, and Samoa. This case-control study included 2781 patients with early-onset AF from 9 studies and identified 4959 controls of European ancestry from the remaining participants. Results were replicated in the UK Biobank (346 546 participants) and the MyCode Study (42 782 participants). EXPOSURES Loss-of-function (LOF) variants in genes at AF loci and common genetic variation across the whole genome. MAIN OUTCOMES AND MEASURES Early-onset AF (defined as AF onset in persons <66 years of age). Due to multiple testing, the significance threshold for the rare variant analysis was P = 4.55 × 10-3. RESULTS Among 2781 participants with early-onset AF (the case group), 72.1% were men, and the mean (SD) age of AF onset was 48.7 (10.2) years. Participants underwent whole-genome sequencing at a mean depth of 37.8 fold and mean genome coverage of 99.1%. At least 1 LOF variant in TTN, the gene encoding the sarcomeric protein titin, was present in 2.1% of case participants compared with 1.1% in control participants (odds ratio [OR], 1.76 [95% CI, 1.04-2.97]). The proportion of individuals with early-onset AF who carried a LOF variant in TTN increased with an earlier age of AF onset (P value for trend, 4.92 × 10-4), and 6.5% of individuals with AF onset prior to age 30 carried a TTN LOF variant (OR, 5.94 [95% CI, 2.64-13.35]; P = 1.65 × 10-5). The association between TTN LOF variants and AF was replicated in an independent study of 1582 patients with early-onset AF (cases) and 41 200 control participants (OR, 2.16 [95% CI, 1.19-3.92]; P = .01). CONCLUSIONS AND RELEVANCE In a case-control study, there was a statistically significant association between an LOF variant in the TTN gene and early-onset AF, with the variant present in a small percentage of participants with early-onset AF (the case group). Further research is necessary to understand whether this is a causal relationship.
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Affiliation(s)
- Seung Hoan Choi
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Weng Lu-Chen
- 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
| | - Carolina Roselli
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Honghuang Lin
- NHLBI and Boston University’s Framingham Heart Study, Framingham, MA, USA
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - M. Benjamin Shoemaker
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Barnard
- Departments of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel I. Chasman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Preventive Medicine and Genetics, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
| | - Christine M. Albert
- Divisions of Preventive and Cardiovascular Medicine, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
| | - Mark Chaffin
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathan R. Tucker
- 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
| | - Jonathan D. Smith
- Departments of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey Gabriel
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lauren Margolin
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marisa A. Shea
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Christian M. Shaffer
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zachary T. Yoneda
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 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
| | - Nicholas L. Smith
- Department of Epidemiology and Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Esteban G. Burchard
- Department of Bioengineering, School of Pharmacy, University of California, San Francisco, CA, USA
| | | | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Thomas W. Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Gonçalo Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - David J. Carey
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | | | - Diane T. Smelser
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | - Cashell E. Jaquish
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - George J. Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Bruce M. Psaty
- Department of Epidemiology and Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dawood Darbar
- Division of Cardiology, Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Susan R. Heckbert
- Department of Epidemiology and Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Mina K. Chung
- Departments of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Dan M. Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emelia J. Benjamin
- NHLBI and Boston University’s Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | | | - Kathryn L. Lunetta
- NHLBI and Boston University’s Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Steven A. Lubitz
- 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
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T. Ellinor
- 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
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, MA, USA
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13
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Raffield LM, Zakai NA, Duan Q, Laurie C, Smith JD, Irvin MR, Doyle MF, Naik RP, Song C, Manichaikul AW, Liu Y, Durda P, Rotter JI, Jenny NS, Rich SS, Wilson JG, Johnson AD, Correa A, Li Y, Nickerson DA, Rice K, Lange EM, Cushman M, Lange LA, Reiner AP. D-Dimer in African Americans: Whole Genome Sequence Analysis and Relationship to Cardiovascular Disease Risk in the Jackson Heart Study. Arterioscler Thromb Vasc Biol 2017; 37:2220-2227. [PMID: 28912365 DOI: 10.1161/atvbaha.117.310073] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/29/2017] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Plasma levels of the fibrinogen degradation product D-dimer are higher among African Americans (AAs) compared with those of European ancestry and higher among women compared with men. Among AAs, little is known of the genetic architecture of D-dimer or the relationship of D-dimer to incident cardiovascular disease. APPROACH AND RESULTS We measured baseline D-dimer in 4163 AAs aged 21 to 93 years from the prospective JHS (Jackson Heart Study) cohort and assessed association with incident cardiovascular disease events. In participants with whole genome sequencing data (n=2980), we evaluated common and rare genetic variants for association with D-dimer. Each standard deviation higher baseline D-dimer was associated with a 20% to 30% increased hazard for incident coronary heart disease, stroke, and all-cause mortality. Genetic variation near F3 was associated with higher D-dimer (rs2022030, β=0.284, P=3.24×10-11). The rs2022030 effect size was nearly 3× larger among women (β=0.373, P=9.06×10-13) than among men (β=0.135, P=0.06; P interaction =0.009). The sex by rs2022030 interaction was replicated in an independent sample of 10 808 multiethnic men and women (P interaction =0.001). Finally, the African ancestral sickle cell variant (HBB rs334) was significantly associated with higher D-dimer in JHS (β=0.507, P=1.41×10-14), and this association was successfully replicated in 1933 AAs (P=2.3×10-5). CONCLUSIONS These results highlight D-dimer as an important predictor of cardiovascular disease risk in AAs and suggest that sex-specific and African ancestral genetic effects of the F3 and HBB loci contribute to the higher levels of D-dimer among women and AAs.
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Affiliation(s)
- Laura M Raffield
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.).
| | - Neil A Zakai
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Qing Duan
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Cecelia Laurie
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Joshua D Smith
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Marguerite R Irvin
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Margaret F Doyle
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Rakhi P Naik
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Ci Song
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Ani W Manichaikul
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Yongmei Liu
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Peter Durda
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Jerome I Rotter
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Nancy S Jenny
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Stephen S Rich
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - James G Wilson
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Andrew D Johnson
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Adolfo Correa
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Yun Li
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Deborah A Nickerson
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Kenneth Rice
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Ethan M Lange
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Mary Cushman
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Leslie A Lange
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
| | - Alex P Reiner
- From the Department of Genetics (L.M.R., Q.D., Y. Li), Department of Biostatistics (Y. Li), and Department of Computer Science (Y. Li), University of North Carolina, Chapel Hill; Department of Pathology & Laboratory Medicine (N.A.Z., M.F.D., P.D., N.S.J., M.C.), and Department of Medicine (N.A.Z., M.C.), Hematology/Oncology Division, Larner College of Medicine at the University of Vermont, Burlington; Department of Biostatistics (C.L., K.R.), Department of Genome Sciences (J.D.S., D.A.N.), and Department of Epidemiology (A.P.R.), University of Washington, Seattle; Department of Epidemiology, University of Alabama, Birmingham (M.R.I.); Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD (R.P.N.); National Heart, Lung, and Blood Institute, Division of Intramural Research, Population Sciences Branch, Bethesda, MD (C.S., A.D.J.); Center for Public Health Genomics, University of Virginia, Charlottesville (A.W.M., S.S.R.); Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC (Y. Liu); Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, CA, and the David Geffen School of Medicine at UCLA (J.I.R.); Department of Physiology and Biophysics (J.G.W.), and Department of Medicine (A.C.), University of Mississippi Medical Center, Jackson; and Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora (E.M.L., L.A.L.)
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Ooi GJ, Doyle L, Tie T, Wentworth JM, Laurie C, Earnest A, Cowley MA, Sikaris K, le Roux CW, Burton PR, O'Brien PE, Brown WA. Weight loss after laparoscopic adjustable gastric band and resolution of the metabolic syndrome and its components. Int J Obes (Lond) 2017; 41:902-908. [PMID: 28262677 DOI: 10.1038/ijo.2017.59] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 02/11/2017] [Accepted: 02/19/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Substantial weight loss in the setting of obesity has considerable metabolic benefits. Yet some studies have shown improvements in obesity-related metabolic comorbidities with more modest weight loss. By closely monitoring patients undergoing bariatric surgery, we aimed to determine the effects of weight loss on the metabolic syndrome and its components and determine the weight loss required for their resolution. METHODS We performed a prospective observational study of obese participants with metabolic syndrome (Adult Treatment Panel III criteria) who underwent laparoscopic adjustable gastric banding. Participants were assessed for all criteria of the metabolic syndrome monthly for the first 9 months, then 3-monthly until 24 months. RESULTS There were 89 participants with adequate longitudinal data. Baseline body mass index was 42.4±6.2 kg m-2 with an average age was 48.2±10.7 years. There were 56 (63%) women. Resolution of the metabolic syndrome occurred in 60 of the 89 participants (67%) at 12 months and 60 of the 75 participants (80%) at 24 months. The mean weight loss when metabolic syndrome resolved was 10.9±7.7% total body weight loss (TBWL). The median weight loss at which prevalence of disease halved was 7.0% TBWL (17.5% excess weight loss (EWL)) for hypertriglyceridaemia; 11% TBWL (26.1-28% EWL) for high-density lipoprotein cholesterol and hyperglycaemia; 20% TBWL (59.5% EWL) for hypertension and 29% TBWL (73.3% EWL) for waist circumference. The odds ratio for resolution of the metabolic syndrome with 10-12.5% TBWL was 2.09 (P=0.025), with increasing probability of resolution with more substantial weight loss. CONCLUSIONS In obese participants with metabolic syndrome, a weight loss target of 10-12.5% TBWL (25-30% EWL) is a reasonable initial goal associated with significant odds of having metabolic benefits. If minimal improvements are seen with this initial target, additional weight loss substantially increases the probability of resolution.
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Affiliation(s)
- G J Ooi
- Centre for Obesity Research and Education, Monash University, Melbourne, Victoria, Australia.,Monash University Department of Surgery, Alfred Hospital, Melbourne, Victoria, Australia
| | - L Doyle
- Centre for Obesity Research and Education, Monash University, Melbourne, Victoria, Australia
| | - T Tie
- Centre for Obesity Research and Education, Monash University, Melbourne, Victoria, Australia.,Monash University Department of Surgery, Alfred Hospital, Melbourne, Victoria, Australia
| | - J M Wentworth
- Centre for Obesity Research and Education, Monash University, Melbourne, Victoria, Australia.,Walter and Eliza Hall Institute, Melbourne University, Parkville, Victoria, Australia
| | - C Laurie
- Centre for Obesity Research and Education, Monash University, Melbourne, Victoria, Australia
| | - A Earnest
- Department of Epidemiology, SPHPM, Monash University, Melbourne, Victoria, Australia
| | - M A Cowley
- MODI, Monash University, Melbourne, Victoria, Australia
| | - K Sikaris
- Melbourne Pathology, East Melbourne, Victoria, Australia
| | - C W le Roux
- Diabetes Complications Research Centre, University College, Dublin, Ireland
| | - P R Burton
- Centre for Obesity Research and Education, Monash University, Melbourne, Victoria, Australia
| | - P E O'Brien
- Centre for Obesity Research and Education, Monash University, Melbourne, Victoria, Australia
| | - W A Brown
- Centre for Obesity Research and Education, Monash University, Melbourne, Victoria, Australia.,Monash University Department of Surgery, Alfred Hospital, Melbourne, Victoria, Australia
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Teerlink CC, Leongamornlert D, Dadaev T, Thomas A, Farnham J, Stephenson RA, Riska S, McDonnell SK, Schaid DJ, Catalona WJ, Zheng SL, Cooney KA, Ray AM, Zuhlke KA, Lange EM, Giles GG, Southey MC, Fitzgerald LM, Rinckleb A, Luedeke M, Maier C, Stanford JL, Ostrander EA, Kaikkonen EM, Sipeky C, Tammela T, Schleutker J, Wiley KE, Isaacs SD, Walsh PC, Isaacs WB, Xu J, Cancel-Tassin G, Cussenot O, Mandal D, Laurie C, Laurie C, Thibodeau SN, Eeles RA, Kote-Jarai Z, Cannon-Albright L. Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21. Hum Genet 2016; 135:923-38. [PMID: 27262462 PMCID: PMC5020907 DOI: 10.1007/s00439-016-1690-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
Previous genome-wide association studies (GWAS) of prostate cancer risk focused on cases unselected for family history and have reported over 100 significant associations. The International Consortium for Prostate Cancer Genetics (ICPCG) has now performed a GWAS of 2511 (unrelated) familial prostate cancer cases and 1382 unaffected controls from 12 member sites. All samples were genotyped on the Illumina 5M+exome single nucleotide polymorphism (SNP) platform. The GWAS identified a significant evidence for association for SNPs in six regions previously associated with prostate cancer in population-based cohorts, including 3q26.2, 6q25.3, 8q24.21, 10q11.23, 11q13.3, and 17q12. Of note, SNP rs138042437 (p = 1.7e(-8)) at 8q24.21 achieved a large estimated effect size in this cohort (odds ratio = 13.3). 116 previously sampled affected relatives of 62 risk-allele carriers from the GWAS cohort were genotyped for this SNP, identifying 78 additional affected carriers in 62 pedigrees. A test for an excess number of affected carriers among relatives exhibited strong evidence for co-segregation of the variant with disease (p = 8.5e(-11)). The majority (92 %) of risk-allele carriers at rs138042437 had a consistent estimated haplotype spanning approximately 100 kb of 8q24.21 that contained the minor alleles of three rare SNPs (dosage minor allele frequencies <1.7 %), rs183373024 (PRNCR1), previously associated SNP rs188140481, and rs138042437 (CASC19). Strong evidence for co-segregation of a SNP on the haplotype further characterizes the haplotype as a prostate cancer predisposition locus.
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Affiliation(s)
- Craig C Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
| | - Daniel Leongamornlert
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Tokhir Dadaev
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Alun Thomas
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - James Farnham
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - Robert A Stephenson
- Department of Urology, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Shaun Riska
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shannon K McDonnell
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - William J Catalona
- Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - S Lilly Zheng
- Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Kathleen A Cooney
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Anna M Ray
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kimberly A Zuhlke
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ethan M Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Melissa C Southey
- Department of Pathology, University of Melbourne, Melbourne, 3010, Australia
| | - Liesel M Fitzgerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, 3004, Australia
| | - Antje Rinckleb
- Department of Urology, University Hospital Ulm, 53179, Ulm, Germany
| | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, 53179, Ulm, Germany
| | - Christiane Maier
- Institute for Human Genetics, University of Ulm, 89081, Ulm, Germany
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, 98109, USA
| | - Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Elina M Kaikkonen
- Department of Medical Biochemistry and Genetics, University of Turku, 20520, Turku, Finland
| | - Csilla Sipeky
- Department of Medical Biochemistry and Genetics, University of Turku, 20520, Turku, Finland
| | - Teuvo Tammela
- Department of Urology, University of Tampere and Tampere University Hospital, 33520, Tampere, Finland
| | - Johanna Schleutker
- Tyks Microbiology and Genetics, Department of Medical Genetics, Turku University Hospital, 20520, Turku, Finland
| | - Kathleen E Wiley
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Sarah D Isaacs
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Patrick C Walsh
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - William B Isaacs
- Brady Urological Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, IL, 60201, USA
| | | | - Olivier Cussenot
- CeRePP, Hopital Tenon, Assistance Publique-Hopitaux de Paris, 75020, Paris, France
| | - Diptasri Mandal
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Cathy Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Stephen N Thibodeau
- Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Lisa Cannon-Albright
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, 84148, USA
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Wasser SK, Brown L, Mailand C, Mondol S, Clark W, Laurie C, Weir BS. CONSERVATION. Genetic assignment of large seizures of elephant ivory reveals Africa's major poaching hotspots. Science 2015; 349:84-7. [PMID: 26089357 PMCID: PMC5535781 DOI: 10.1126/science.aaa2457] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 05/22/2015] [Indexed: 11/02/2022]
Abstract
Poaching of elephants is now occurring at rates that threaten African populations with extinction. Identifying the number and location of Africa's major poaching hotspots may assist efforts to end poaching and facilitate recovery of elephant populations. We genetically assign origin to 28 large ivory seizures (≥0.5 metric tons) made between 1996 and 2014, also testing assignment accuracy. Results suggest that the major poaching hotspots in Africa may be currently concentrated in as few as two areas. Increasing law enforcement in these two hotspots could help curtail future elephant losses across Africa and disrupt this organized transnational crime.
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Affiliation(s)
- S K Wasser
- Center for Conservation Biology, Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA.
| | - L Brown
- Department of Biostatistics, University of Washington, Box 357232, Seattle, WA 98195-7232, USA
| | - C Mailand
- Center for Conservation Biology, Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - S Mondol
- Center for Conservation Biology, Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - W Clark
- INTERPOL, Environmental Security Sub-Directorate (ENS), Lyon, France
| | - C Laurie
- Department of Biostatistics, University of Washington, Box 357232, Seattle, WA 98195-7232, USA
| | - B S Weir
- Department of Biostatistics, University of Washington, Box 357232, Seattle, WA 98195-7232, USA
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Abstract
BACKGROUND How to map quantitative trait loci (QTL) with epistasis efficiently and reliably has been a persistent problem for QTL mapping analysis. There are a number of difficulties for studying epistatic QTL. Linkage can impose a significant challenge for finding epistatic QTL reliably. If multiple QTL are in linkage and have interactions, searching for QTL can become a very delicate issue. A commonly used strategy that performs a two-dimensional genome scan to search for a pair of QTL with epistasis can suffer from low statistical power and also may lead to false identification due to complex linkage disequilibrium and interaction patterns. RESULTS To tackle the problem of complex interaction of multiple QTL with linkage, we developed a three-stage search strategy. In the first stage, main effect QTL are searched and mapped. In the second stage, epistatic QTL that interact significantly with other identified QTL are searched. In the third stage, new epistatic QTL are searched in pairs. This strategy is based on the consideration that most genetic variance is due to the main effects of QTL. Thus by first mapping those main-effect QTL, the statistical power for the second and third stages of analysis for mapping epistatic QTL can be maximized. The search for main effect QTL is robust and does not bias the search for epistatic QTL due to a genetic property associated with the orthogonal genetic model that the additive and additive by additive variances are independent despite of linkage. The model search criterion is empirically and dynamically evaluated by using a score-statistic based resampling procedure. We demonstrate through simulations that the method has good power and low false positive in the identification of QTL and epistasis. CONCLUSION This method provides an effective and powerful solution to map multiple QTL with complex epistatic pattern. The method has been implemented in the user-friendly computer software Windows QTL Cartographer. This will greatly facilitate the application of the method for QTL mapping data analysis.
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Affiliation(s)
- Cecelia Laurie
- Department of Mathematics, University of Alabama, Tuscaloosa AL, USA. .,Department of Biostatistics, University of Washington, Seattle WA, USA.
| | - Shengchu Wang
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh NC, 27695-7566, USA.
| | - Luciana Aparecida Carlini-Garcia
- Instituto Agronômico de Campinas, Centro de Grãos e Fibras, Campinas SP, Brazil. .,APTA Regional, Pólo Centro Sul, Piracicaba SP, Brazil.
| | - Zhao-Bang Zeng
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh NC, 27695-7566, USA. .,Department of Biological Sciences, North Carolina State University, Raleigh NC, USA.
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Schneiter S, Warrier R, Lefkovits L, Laurie C, O’Brien P, Taylor A. Effects of Weight Loss on Left Ventricle and Pericardial Fat Assessed with Cardiac Magnetic Resonance Imaging in Morbid Obesity. Heart Lung Circ 2010. [DOI: 10.1016/j.hlc.2010.06.434] [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: 11/30/2022]
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Abstract
For finite populations, differences in individual histories can cause between-locus allelic dependencies even for unlinked loci. The main motivation for this study is to quantify the effect of such dependencies on genotypic match probabilities. We compare the two-locus match probability, the probability that two individuals (four gametes) chosen at random will have the same genotype at both loci, with the probability computed as the product of the one-locus match probabilities. It is demonstrated that the product rule probability always underestimates the two-locus match probability. For highly mutable minisatellite loci, these probabilities can differ by an order of magnitude or more. A simplified three-locus problem is explored, providing evidence that the degree of under-estimation worsens for more loci.
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Affiliation(s)
- Cecelia Laurie
- Department of Mathematics, University of Alabama, Tuscaloosa, AL 35487-0350, USA.
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Abstract
In addition to the genes involved in tetracycline resistance, the loop region of the composite transposon Tn10 contains two other known genes, tetC and tetD, whose functions are unclear. Using primarily a genetic approach, we examined tetCD gene expression and regulation. The tetC gene product, TetC, is a diffusible repressor of both tetC and tetD transcription. Despite an earlier claim by others, we do not detect induction of either tetC or tetD by tetracycline (Tc) or several of its analogs. Although the 5' ends of the tetC and tetD messages overlap due to transcription from convergent promoters, we find no evidence for anti-sense RNA control. The operator for the TetC repressor has been localized. We also demonstrate that transcription from the tetD promoter probably terminates within IS10-Right and does not apparently interfere with Tn10 or IS10-Right transposition or its regulation.
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Affiliation(s)
- C M Pepe
- Department of Microbiology and Molecular Genetics, University of California, Los Angeles, USA
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Abstract
In three experiments, the effect of additional "contextual" elements on the discrimination of the orientation of linear and curvilinear segments was investigated with 4-month-old infants. In Experiment 1, paired visual matrices (one which contained some irregularity in orientation of internal elements, vs one which contained no irregularities) were presented. Infants detected irregular matrices significantly better than chance, but such detection was not aided by contextual elements. Discrimination of orientation in Experiment 2 was assessed with a paired-comparison familiarization-novelty paradigm. It was found that the addition of elements here significantly aided discrimination of linear segment orientation, but not curvilinear segment orientation. Experiment 3 investigated why this effect was not found for curvilinear segments; after equating the curvilinear stimuli to linear ones used in Experiment 2 with respect to the closedness of figure, discrimination of curvilinear orientation was observed.
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