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Rao H, Weiss MC, Moon JY, Perreira KM, Daviglus ML, Kaplan R, North KE, Argos M, Fernández-Rhodes L, Sofer T. Advancements in genetic research by the Hispanic Community Health Study/Study of Latinos: A 10-year retrospective review. HGG ADVANCES 2025; 6:100376. [PMID: 39473183 PMCID: PMC11754138 DOI: 10.1016/j.xhgg.2024.100376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 10/24/2024] [Accepted: 10/24/2024] [Indexed: 11/14/2024] Open
Abstract
The Hispanic Community Health Study/Study of Latinos (HCHS/SOL) is a multicenter, longitudinal cohort study designed to evaluate environmental, lifestyle, and genetic risk factors as they relate to cardiometabolic and other chronic diseases among Hispanic/Latino populations in the United States. Since the study's inception in 2008, as a result of the study's robust genetic measures, HCHS/SOL has facilitated major contributions to the field of genetic research. This 10-year retrospective review highlights the major findings for genotype-phenotype relationships and advancements in statistical methods owing to the HCHS/SOL. Furthermore, we discuss the ethical and societal challenges of genetic research, especially among Hispanic/Latino adults in the United States. Continued genetic research, ancillary study expansion, and consortia collaboration through HCHS/SOL will further drive knowledge and advancements in human genetics research.
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Affiliation(s)
- Hridya Rao
- Department of Biobehavioral Health, Pennsylvania State University, University Park, PA, USA
| | - Margaret C Weiss
- Department of Epidemiology and Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL, USA
| | - Jee Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Krista M Perreira
- Department of Social Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Maria Argos
- Department of Epidemiology and Biostatistics, School of Public Health, University of Illinois Chicago, Chicago, IL, USA; Department of Environmental Health, School of Public Health, Boston University, Boston, MA, USA
| | | | - Tamar Sofer
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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2
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Zheng G, Chattopadhyay S, Sundquist J, Sundquist K, Ji J. Antihypertensive drug targets and breast cancer risk: a two-sample Mendelian randomization study. Eur J Epidemiol 2024; 39:535-548. [PMID: 38396187 PMCID: PMC11219410 DOI: 10.1007/s10654-024-01103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/15/2024] [Indexed: 02/25/2024]
Abstract
Findings on the correlation between the use of antihypertensive medication and the risk of breast cancer (BC) have been inconsistent. We performed a two-sample Mendelian randomization (MR) using instrumental variables to proxy changes in gene expressions of antihypertensive medication targets to interrogate this. Genetic instruments for expression of antihypertensive drug target genes were identified with expression quantitative trait loci in blood, which should be associated with systolic blood pressure to proxy for the effect of antihypertensive drug. The association between genetic variants and BC risk were obtained from genome-wide association study summary statistics. The summary-based MR was employed to estimate the drug effects on BC risk. We further performed sensitivity analyses to confirm the discovered MR associations such as assessment of horizontal pleiotropy, colocalization, and multiple tissue enrichment analyses. The overall BC risk was only associated with SLC12A2 gene expression at a Bonferroni-corrected threshold. One standard deviation (SD) decrease of SLC12A2 gene expression in blood was associated with a decrease of 1.12 (95%CI, 0.80-1.58) mmHg of systolic blood pressure, but a 16% increased BC risk (odds ratio, 1.16, 95% confidential interval, 1.06-1.28). This signal was further observed for estrogen receptor positive (ER +) BC (1.17, 1.06-1.28). In addition, one SD decrease in expression of PDE1B in blood was associated with 7% decreased risk of ER + BC (0.93, 0.90-0.97). We detected no evidence of horizontal pleiotropy for these associations and the probability of the causal variants being shared between the gene expression and BC risk was 81.5, 40.5 and 66.8%, respectively. No significant association was observed between other target gene expressions and BC risk. Changes in expression of SLC12A2 and PDE1B mediated possibly via antihypertensive drugs may result in increased and decreased BC risk, respectively.
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Affiliation(s)
- Guoqiao Zheng
- Center for Primary Health Care Research, Lund University/Region Skåne, Jan Waldenströms Gata 35, 205 02, Malmö, Sweden.
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University/Region Skåne, Jan Waldenströms Gata 35, 205 02, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Community-Based Healthcare Research and Education (CoHRE), Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University/Region Skåne, Jan Waldenströms Gata 35, 205 02, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Community-Based Healthcare Research and Education (CoHRE), Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan
| | - Jianguang Ji
- Center for Primary Health Care Research, Lund University/Region Skåne, Jan Waldenströms Gata 35, 205 02, Malmö, Sweden.
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3
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Pan J, Sun J, Goncalves I, Kessler M, Hao Y, Engström G. Red cell distribution width and its polygenic score in relation to mortality and cardiometabolic outcomes. Front Cardiovasc Med 2023; 10:1294218. [PMID: 38054099 PMCID: PMC10694461 DOI: 10.3389/fcvm.2023.1294218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023] Open
Abstract
Introduction Elevated red cell distribution width (RDW) has been associated with a range of health outcomes. This study aims to examine prognostic and etiological roles of RDW levels, both phenotypic and genetic predisposition, in predicting cardiovascular outcomes, diabetes, chronic kidney disease (CKD) and mortality. Methods We studied 27,141 middle-aged adults from the Malmö Diet and Cancer study (MDCS) with a mean follow up of 21 years. RDW was measured with a hematology analyzer on whole blood samples. Polygenic scores for RDW (PGS-RDW) were constructed for each participant using genetic data in MDCS and published summary statistics from genome-wide association study of RDW (n = 408,112). Cox proportional hazards regression was used to assess associations between RDW, PGS-RDW and cardiovascular outcomes, diabetes, CKD and mortality, respectively. Results PGS-RDW was significantly associated with RDW (Pearson's correlation coefficient = 0.133, p < 0.001). RDW was significantly associated with incidence of stroke (hazard ratio (HR) per 1 standard deviation = 1.06, 95% confidence interval (CI): 1.02-1.10, p = 0.003), atrial fibrillation (HR = 1.09, 95% CI: 1.06-1.12, p < 0.001), heart failure (HR = 1.13, 95% CI: 1.08-1.19, p < 0.001), venous thromboembolism (HR = 1.21, 95% CI: 1.15-1.28, p < 0.001), diabetes (HR = 0.87, 95% CI: 0.84-0.90, p < 0.001), CKD (HR = 1.08, 95% CI: 1.03-1.13, p = 0.004) and all-cause mortality (HR = 1.18, 95% CI: 1.16-1.20, p < 0.001). However, PGS-RDW was significantly associated with incidence of diabetes (HR = 0.96, 95% CI: 0.94-0.99, p = 0.01), but not with any other tested outcomes. Discussion RDW is associated with mortality and incidence of cardiovascular diseases, but a significant association between genetically determined RDW and incident cardiovascular diseases were not observed. However, both RDW and PGS-RDW were inversely associated with incidence of diabetes, suggesting a putative causal relationship. The relationship with incidence of diabetes needs to be further studied.
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Affiliation(s)
- Jingxue Pan
- Division of Child Healthcare, Department of Paediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Jiangming Sun
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | | | | | - Yan Hao
- Division of Child Healthcare, Department of Paediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gunnar Engström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- Regeneron Genetics Center, Tarrytown, NY, United States
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4
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Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525428. [PMID: 36747810 PMCID: PMC9900832 DOI: 10.1101/2023.01.25.525428] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
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Affiliation(s)
- Goo Jun
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
| | - Adam C English
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Ginger A Metcalf
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jianzhi Yang
- University of Southern California, Los Angeles, CA, USA
| | | | | | - Vipin K Menon
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | | | | | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - John A Lane
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Tom Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Hyun Min Kang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Sejal Salvi
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Qingchang Meng
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Hua Shen
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Divya Pasham
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Sravya Bhamidipati
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kavya Kottapalli
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Donna K. Arnett
- Department of Epidemiology, University of Kentucky College of Public Health
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC
| | - Paul L. Auer
- Division of Biostatistics and Cancer Center, Medical College of Wisconsin, Milwaukee WI
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas, Rio Grande Valley School of Medicine, Brownsville, TX
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Joanne E. Curran
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tasha Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson St., Denver, CO, 80206, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | | | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco
| | - Robert Kaplan
- Department of epidemiology and population health, Albert Einstein College of Medicine, Bronx NY USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco CA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen T. McGarvey
- Department of Epidemiology, International Health Institute and Department of Anthropology, Brown University
| | - Courtney Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - S. Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephen S. Rich
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University Bloomberg, School of Public Health, Baltimore, MD, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School
- Cardiovascular Division, Brigham & Women’s Hospital, Harvard University
- Howard Hughes Medical Institute, Harvard University
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA
| | - Jennifer A. Smith
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Lisa R. Yanek
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Ryan Kim
- Psomagen, Inc.,Rockville, Maryland, USA
| | | | | | | | - James Luo
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Goncalo Abecasis
- Regeneron Genetics Center
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Fritz J Sedlazeck
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA
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5
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Verma A, Huffman JE, Gao L, Minnier J, Wu WC, Cho K, Ho YL, Gorman BR, Pyarajan S, Rajeevan N, Garcon H, Joseph J, McGeary JE, Suzuki A, Reaven PD, Wan ES, Lynch JA, Petersen JM, Meigs JB, Freiberg MS, Gatsby E, Lynch KE, Zekavat SM, Natarajan P, Dalal S, Jhala DN, Arjomandi M, Bonomo RA, Thompson TK, Pathak GA, Zhou JJ, Donskey CJ, Madduri RK, Wells QS, Gelernter J, Huang RDL, Polimanti R, Chang KM, Liao KP, Tsao PS, Sun YV, Wilson PWF, O’Donnell CJ, Hung AM, Gaziano JM, Hauger RL, Iyengar SK, Luoh SW. Association of Kidney Comorbidities and Acute Kidney Failure With Unfavorable Outcomes After COVID-19 in Individuals With the Sickle Cell Trait. JAMA Intern Med 2022; 182:796-804. [PMID: 35759254 PMCID: PMC9237798 DOI: 10.1001/jamainternmed.2022.2141] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Importance Sickle cell trait (SCT), defined as the presence of 1 hemoglobin beta sickle allele (rs334-T) and 1 normal beta allele, is prevalent in millions of people in the US, particularly in individuals of African and Hispanic ancestry. However, the association of SCT with COVID-19 is unclear. Objective To assess the association of SCT with the prepandemic health conditions in participants of the Million Veteran Program (MVP) and to assess the severity and sequelae of COVID-19. Design, Setting, and Participants COVID-19 clinical data include 2729 persons with SCT, of whom 353 had COVID-19, and 129 848 SCT-negative individuals, of whom 13 488 had COVID-19. Associations between SCT and COVID-19 outcomes were examined using firth regression. Analyses were performed by ancestry and adjusted for sex, age, age squared, and ancestral principal components to account for population stratification. Data for the study were collected between March 2020 and February 2021. Exposures The hemoglobin beta S (HbS) allele (rs334-T). Main Outcomes and Measures This study evaluated 4 COVID-19 outcomes derived from the World Health Organization severity scale and phenotypes derived from International Classification of Diseases codes in the electronic health records. Results Of the 132 577 MVP participants with COVID-19 data, mean (SD) age at the index date was 64.8 (13.1) years. Sickle cell trait was present in 7.8% of individuals of African ancestry and associated with a history of chronic kidney disease, diabetic kidney disease, hypertensive kidney disease, pulmonary embolism, and cerebrovascular disease. Among the 4 clinical outcomes of COVID-19, SCT was associated with an increased COVID-19 mortality in individuals of African ancestry (n = 3749; odds ratio, 1.77; 95% CI, 1.13 to 2.77; P = .01). In the 60 days following COVID-19, SCT was associated with an increased incidence of acute kidney failure. A counterfactual mediation framework estimated that on average, 20.7% (95% CI, -3.8% to 56.0%) of the total effect of SCT on COVID-19 fatalities was due to acute kidney failure. Conclusions and Relevance In this genetic association study, SCT was associated with preexisting kidney comorbidities, increased COVID-19 mortality, and kidney morbidity.
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Affiliation(s)
- Anurag Verma
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania
- Perelman School of Medicine, Department of Medicine, University of Pennsylvania, Philadelphia
| | | | - Lina Gao
- Knight Cancer Institute, Biostatistics Shared Resource, Oregon Health & Science University, Portland
- VA Portland Health Care System, Portland, Oregon
| | - Jessica Minnier
- VA Portland Health Care System, Portland, Oregon
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland
- Knight Cancer Institute, Biostatistics Shared Resource, Oregon Health & Science University, Portland
| | - Wen-Chih Wu
- Department of Medicine, Cardiology, Providence VA Healthcare System, Providence, Rhode Island
- Alpert Medical School & School of Public Health, Brown University, Providence, Rhode Island
| | - Kelly Cho
- MAVERIC, VA Boston Healthcare System, Boston, Massachusetts
- Medicine, Aging, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yuk-Lam Ho
- MAVERIC, VA Boston Healthcare System, Boston, Massachusetts
| | | | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Nallakkandi Rajeevan
- Yale Center for Medical Informatics, Yale School of Medicine, New Haven, Connecticut
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven
| | - Helene Garcon
- MAVERIC, VA Boston Healthcare System, Boston, Massachusetts
| | - Jacob Joseph
- Department of Medicine, VA Boston Healthcare System, Boston, Massachusetts
- Brigham & Women’s Hospital, Boston, Massachusetts
| | - John E. McGeary
- Department of Psychiatry and Human Behavior, Providence VA Medical Center, Providence, Rhode Island
- Brown University Medical School, Providence, Rhode Island
| | - Ayako Suzuki
- Department of Medicine, Gastroenterology, Durham VA Medical Center, Durham, North Carolina
- Department of Medicine, Gastroenterology, Duke University, Durham, North Carolina
| | - Peter D. Reaven
- Department of Medicine, Phoenix VA Healthcare System, Phoenix, Arizona
- University of Arizona, Phoenix
| | - Emily S. Wan
- Department of Medicine, Pulmonary, Critical Care, Sleep, and Allergy Section, VA Boston Healthcare System, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham & Women’s Hospital, Boston, Massachusetts
| | - Julie A. Lynch
- VA Informatics & Computing Infrastructure, VA Salt Lake City Utah & University of Utah, School of Medicine, Salt Lake City
| | - Jeffrey M. Petersen
- Pathology and Laboratory Medicine, Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - James B. Meigs
- Medicine, General Internal Medicine, Massachusetts General Hospital, Boston
| | | | - Elise Gatsby
- VA Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, Utah
| | - Kristine E. Lynch
- VA Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, Utah
- Internal Medicine, Epidemiology, University of Utah School of Medicine, Salt Lake City
| | - Seyedeh Maryam Zekavat
- Computational Biology & Bioinformatics, Yale School of Medicine, New Haven, Connecticut
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Clinical Data Science Research Group, ORD, Portland VA Medical Center, Portland, Oregon
| | - Sharvari Dalal
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Pathology and Laboratory Medicine, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania
| | - Darshana N. Jhala
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Pathology and Laboratory Medicine, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania
| | - Mehrdad Arjomandi
- Medicine, Pulmonary and Critical Care, San Francisco VA Healthcare System, San Francisco, California
- University of California San Francisco
| | - Robert A. Bonomo
- Cleveland VA Medical Center, Cleveland, Ohio
- Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - Gita A. Pathak
- Department of Psychiatry, Division of Human Genetics, Yale School of Medicine, New Haven, Connecticut
- VA Connecticut Healthcare System, West Haven
| | - Jin J. Zhou
- Medicine, University of California, Los Angeles
- Epidemiology and Biostatistics, University of Arizona, Phoenix
| | - Curtis J. Donskey
- Infectious Disease Section, Louis Stokes Cleveland VA, Cleveland, Ohio
- Case Western Reserve University, Cleveland, Ohio
| | - Ravi K. Madduri
- Data Science and Learning, Argonne National Laboratory, Lemont, Illinois
| | - Quinn S. Wells
- Departments of Medicine, Biomedical Informatics, and Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joel Gelernter
- VA Connecticut Healthcare System, West Haven
- Psychiatry, Human Genetics, Yale University School of Medicine, West Haven, Connecticut
| | | | - Renato Polimanti
- Departments of Medicine, Biomedical Informatics, and Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
- Psychiatry, Human Genetics, Yale University School of Medicine, West Haven, Connecticut
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Katherine P. Liao
- Medicine, Rheumatology, VA Boston Healthcare System, Boston, Massachusetts
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine & Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Philip S. Tsao
- Precision Medicine, VA Palo Alto Health Care System, Palo Alto, California
| | - Yan V. Sun
- Epidemiology, Emory University School of Public Health, Atlanta, Georgia
- Atlanta VA Health Care System, Decatur, Georgia
| | - Peter W. F. Wilson
- Atlanta VA Health Care System, Decatur, Georgia
- Emory University School of Medicine, Atlanta, Georgia
| | | | - Adriana M. Hung
- Vanderbilt University Medical Center, Nashville, Tennessee
- Nashville VA Medical Center, Nashville, Tennessee
| | - J. Michael Gaziano
- VA Boston Health Care System, Boston, Massachusetts
- Medicine, Harvard Medical School, Boston, Massachusetts
| | - Richard L. Hauger
- Center of Excellence for Stress & Mental Health, VA San Diego Healthcare System, San Diego, California
- Center for Behavioral Genetics of Aging, University of California, San Diego, La Jolla
| | - Sudha K. Iyengar
- Departments of Population and Quantitative Health Sciences, Ophthalmology and Visual Sciences and Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, Oregon
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland
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6
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Tängdén T, Gustafsson S, Rao AS, Ingelsson E. A genome-wide association study in a large community-based cohort identifies multiple loci associated with susceptibility to bacterial and viral infections. Sci Rep 2022; 12:2582. [PMID: 35173190 PMCID: PMC8850418 DOI: 10.1038/s41598-022-05838-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 01/14/2022] [Indexed: 12/21/2022] Open
Abstract
There is limited data on host-specific genetic determinants of susceptibility to bacterial and viral infections. Genome-wide association studies using large population cohorts can be a first step towards identifying patients prone to infectious diseases and targets for new therapies. Genetic variants associated with clinically relevant entities of bacterial and viral infections (e.g., abdominal infections, respiratory infections, and sepsis) in 337,484 participants of the UK Biobank cohort were explored by genome-wide association analyses. Cases (n = 81,179) were identified based on ICD-10 diagnosis codes of hospital inpatient and death registries. Functional annotation was performed using gene expression (eQTL) data. Fifty-seven unique genome-wide significant loci were found, many of which are novel in the context of infectious diseases. Some of the detected genetic variants were previously reported associated with infectious, inflammatory, autoimmune, and malignant diseases or key components of the immune system (e.g., white blood cells, cytokines). Fine mapping of the HLA region revealed significant associations with HLA-DQA1, HLA-DRB1, and HLA-DRB4 locus alleles. PPP1R14A showed strong colocalization with abdominal infections and gene expression in sigmoid and transverse colon, suggesting causality. Shared significant loci across infections and non-infectious phenotypes in the UK Biobank cohort were found, suggesting associations for example between SNPs identified for abdominal infections and CRP, rheumatoid arthritis, and diabetes mellitus. We report multiple loci associated with bacterial and viral infections. A better understanding of the genetic determinants of bacterial and viral infections can be useful to identify patients at risk and in the development of new drugs.
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Affiliation(s)
- Thomas Tängdén
- Infection Medicine, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
| | - Stefan Gustafsson
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Abhiram S Rao
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, 94305, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, 94305, USA
| | - Erik Ingelsson
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, 94305, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, 94305, USA
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7
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Little A, Hu Y, Sun Q, Jain D, Broome J, Chen MH, Thibord F, McHugh C, Surendran P, Blackwell TW, Brody JA, Bhan A, Chami N, de Vries PS, Ekunwe L, Heard-Costa N, Hobbs BD, Manichaikul A, Moon JY, Preuss MH, Ryan K, Wang Z, Wheeler M, Yanek LR, Abecasis GR, Almasy L, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Choquet H, Correa A, Curran JE, Faraday N, Fornage M, Glahn DC, Hou L, Jorgenson E, Kooperberg C, Lewis JP, Lloyd-Jones DM, Loos RJF, Min YI, Mitchell BD, Morrison AC, Nickerson DA, North KE, O'Connell JR, Pankratz N, Psaty BM, Vasan RS, Rich SS, Rotter JI, Smith AV, Smith NL, Tang H, Tracy RP, Conomos MP, Laurie CA, Mathias RA, Li Y, Auer PL, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Thornton T, Reiner AP, Johnson AD, Raffield LM. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative. Hum Mol Genet 2022; 31:347-361. [PMID: 34553764 PMCID: PMC8825339 DOI: 10.1093/hmg/ddab252] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022] Open
Abstract
Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.
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Affiliation(s)
- Amarise Little
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Caitlin McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | | | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Paul S de Vries
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nancy Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ani Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Yuan-I Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
- Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA 98101, USA
- Department of Veterans Affairs Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, WA 98108, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT 05446, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | | | - Timothy Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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8
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Venkataraman GR, DeBoever C, Tanigawa Y, Aguirre M, Ioannidis AG, Mostafavi H, Spencer CCA, Poterba T, Bustamante CD, Daly MJ, Pirinen M, Rivas MA. Bayesian model comparison for rare-variant association studies. Am J Hum Genet 2021; 108:2354-2367. [PMID: 34822764 PMCID: PMC8715195 DOI: 10.1016/j.ajhg.2021.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
Whole-genome sequencing studies applied to large populations or biobanks with extensive phenotyping raise new analytic challenges. The need to consider many variants at a locus or group of genes simultaneously and the potential to study many correlated phenotypes with shared genetic architecture provide opportunities for discovery not addressed by the traditional one variant, one phenotype association study. Here, we introduce a Bayesian model comparison approach called MRP (multiple rare variants and phenotypes) for rare-variant association studies that considers correlation, scale, and direction of genetic effects across a group of genetic variants, phenotypes, and studies, requiring only summary statistic data. We apply our method to exome sequencing data (n = 184,698) across 2,019 traits from the UK Biobank, aggregating signals in genes. MRP demonstrates an ability to recover signals such as associations between PCSK9 and LDL cholesterol levels. We additionally find MRP effective in conducting meta-analyses in exome data. Non-biomarker findings include associations between MC1R and red hair color and skin color, IL17RA and monocyte count, and IQGAP2 and mean platelet volume. Finally, we apply MRP in a multi-phenotype setting; after clustering the 35 biomarker phenotypes based on genetic correlation estimates, we find that joint analysis of these phenotypes results in substantial power gains for gene-trait associations, such as in TNFRSF13B in one of the clusters containing diabetes- and lipid-related traits. Overall, we show that the MRP model comparison approach improves upon useful features from widely used meta-analysis approaches for rare-variant association analyses and prioritizes protective modifiers of disease risk.
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Affiliation(s)
| | - Christopher DeBoever
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Yosuke Tanigawa
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Matthew Aguirre
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | | | | | - Timothy Poterba
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland; Department of Public Health, University of Helsinki, Helsinki 00014, Finland; Department of Mathematics and Statistics, University of Helsinki, Helsinki 00014, Finland.
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
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9
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Simonin-Wilmer I, Orozco-del-Pino P, Bishop DT, Iles MM, Robles-Espinoza CD. An Overview of Strategies for Detecting Genotype-Phenotype Associations Across Ancestrally Diverse Populations. Front Genet 2021; 12:703901. [PMID: 34804113 PMCID: PMC8602802 DOI: 10.3389/fgene.2021.703901] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) have been very successful at identifying genetic variants influencing a large number of traits. Although the great majority of these studies have been performed in European-descent individuals, it has been recognised that including populations with differing ancestries enhances the potential for identifying causal SNPs due to their differing patterns of linkage disequilibrium. However, when individuals from distinct ethnicities are included in a GWAS, it is necessary to implement a number of control steps to ensure that the identified associations are real genotype-phenotype relationships. In this Review, we discuss the analyses that are required when performing multi-ethnic studies, including methods for determining ancestry at the global and local level for sample exclusion, controlling for ancestry in association testing, and post-GWAS interrogation methods such as genomic control and meta-analysis. We hope that this overview provides a primer for those researchers interested in including distinct populations in their studies.
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Affiliation(s)
- Irving Simonin-Wilmer
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Queretaro, Mexico
| | | | - D. Timothy Bishop
- Leeds Institute for Data Analytics and Leeds Institute of Medical Research at St. James’s, University of Leeds, Leeds, United Kingdom
| | - Mark M. Iles
- Leeds Institute for Data Analytics and Leeds Institute of Medical Research at St. James’s, University of Leeds, Leeds, United Kingdom
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Queretaro, Mexico
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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10
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Hu Y, Bien SA, Nishimura KK, Haessler J, Hodonsky CJ, Baldassari AR, Highland HM, Wang Z, Preuss M, Sitlani CM, Wojcik GL, Tao R, Graff M, Huckins LM, Sun Q, Chen MH, Mousas A, Auer PL, Lettre G, Tang W, Qi L, Thyagarajan B, Buyske S, Fornage M, Hindorff LA, Li Y, Lin D, Reiner AP, North KE, Loos RJF, Raffield LM, Peters U, Avery CL, Kooperberg C. Multi-ethnic genome-wide association analyses of white blood cell and platelet traits in the Population Architecture using Genomics and Epidemiology (PAGE) study. BMC Genomics 2021; 22:432. [PMID: 34107879 PMCID: PMC8191001 DOI: 10.1186/s12864-021-07745-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Circulating white blood cell and platelet traits are clinically linked to various disease outcomes and differ across individuals and ancestry groups. Genetic factors play an important role in determining these traits and many loci have been identified. However, most of these findings were identified in populations of European ancestry (EA), with African Americans (AA), Hispanics/Latinos (HL), and other races/ethnicities being severely underrepresented. RESULTS We performed ancestry-combined and ancestry-specific genome-wide association studies (GWAS) for white blood cell and platelet traits in the ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) Study, including 16,201 AA, 21,347 HL, and 27,236 EA participants. We identified six novel findings at suggestive significance (P < 5E-8), which need confirmation, and independent signals at six previously established regions at genome-wide significance (P < 2E-9). We confirmed multiple previously reported genome-wide significant variants in the single variant association analysis and multiple genes using PrediXcan. Evaluation of loci reported from a Euro-centric GWAS indicated attenuation of effect estimates in AA and HL compared to EA populations. CONCLUSIONS Our results highlighted the potential to identify ancestry-specific and ancestry-agnostic variants in participants with diverse backgrounds and advocate for continued efforts in improving inclusion of racially/ethnically diverse populations in genetic association studies for complex traits.
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Affiliation(s)
- Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Katherine K Nishimura
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chani J Hodonsky
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Antoine R Baldassari
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | | | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- The Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Quan Sun
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ming-Huei Chen
- The Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | - Abdou Mousas
- Montreal Heart Institute, Montreal, Quebec, Canada
| | - Paul L Auer
- School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Weihong Tang
- School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Lihong Qi
- School of Medicine, University of California Davis, Davis, CA, USA
| | | | - Steve Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, NJ, USA
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, the University of Texas Health Science Center, Houston, TX, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, NIH National Human Genome Research Institute, Bethesda, MD, USA
| | - Yun Li
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Danyu Lin
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura M Raffield
- Department of Genetics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christy L Avery
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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11
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Chen J, Spracklen CN, Marenne G, Varshney A, Corbin LJ, Luan J, Willems SM, Wu Y, Zhang X, Horikoshi M, Boutin TS, Mägi R, Waage J, Li-Gao R, Chan KHK, Yao J, Anasanti MD, Chu AY, Claringbould A, Heikkinen J, Hong J, Hottenga JJ, Huo S, Kaakinen MA, Louie T, März W, Moreno-Macias H, Ndungu A, Nelson SC, Nolte IM, North KE, Raulerson CK, Ray D, Rohde R, Rybin D, Schurmann C, Sim X, Southam L, Stewart ID, Wang CA, Wang Y, Wu P, Zhang W, Ahluwalia TS, Appel EVR, Bielak LF, Brody JA, Burtt NP, Cabrera CP, Cade BE, Chai JF, Chai X, Chang LC, Chen CH, Chen BH, Chitrala KN, Chiu YF, de Haan HG, Delgado GE, Demirkan A, Duan Q, Engmann J, Fatumo SA, Gayán J, Giulianini F, Gong JH, Gustafsson S, Hai Y, Hartwig FP, He J, Heianza Y, Huang T, Huerta-Chagoya A, Hwang MY, Jensen RA, Kawaguchi T, Kentistou KA, Kim YJ, Kleber ME, Kooner IK, Lai S, Lange LA, Langefeld CD, Lauzon M, Li M, Ligthart S, Liu J, Loh M, Long J, Lyssenko V, Mangino M, Marzi C, Montasser ME, Nag A, Nakatochi M, Noce D, Noordam R, Pistis G, Preuss M, Raffield L, et alChen J, Spracklen CN, Marenne G, Varshney A, Corbin LJ, Luan J, Willems SM, Wu Y, Zhang X, Horikoshi M, Boutin TS, Mägi R, Waage J, Li-Gao R, Chan KHK, Yao J, Anasanti MD, Chu AY, Claringbould A, Heikkinen J, Hong J, Hottenga JJ, Huo S, Kaakinen MA, Louie T, März W, Moreno-Macias H, Ndungu A, Nelson SC, Nolte IM, North KE, Raulerson CK, Ray D, Rohde R, Rybin D, Schurmann C, Sim X, Southam L, Stewart ID, Wang CA, Wang Y, Wu P, Zhang W, Ahluwalia TS, Appel EVR, Bielak LF, Brody JA, Burtt NP, Cabrera CP, Cade BE, Chai JF, Chai X, Chang LC, Chen CH, Chen BH, Chitrala KN, Chiu YF, de Haan HG, Delgado GE, Demirkan A, Duan Q, Engmann J, Fatumo SA, Gayán J, Giulianini F, Gong JH, Gustafsson S, Hai Y, Hartwig FP, He J, Heianza Y, Huang T, Huerta-Chagoya A, Hwang MY, Jensen RA, Kawaguchi T, Kentistou KA, Kim YJ, Kleber ME, Kooner IK, Lai S, Lange LA, Langefeld CD, Lauzon M, Li M, Ligthart S, Liu J, Loh M, Long J, Lyssenko V, Mangino M, Marzi C, Montasser ME, Nag A, Nakatochi M, Noce D, Noordam R, Pistis G, Preuss M, Raffield L, Rasmussen-Torvik LJ, Rich SS, Robertson NR, Rueedi R, Ryan K, Sanna S, Saxena R, Schraut KE, Sennblad B, Setoh K, Smith AV, Sparsø T, Strawbridge RJ, Takeuchi F, Tan J, Trompet S, van den Akker E, van der Most PJ, Verweij N, Vogel M, Wang H, Wang C, Wang N, Warren HR, Wen W, Wilsgaard T, Wong A, Wood AR, Xie T, Zafarmand MH, Zhao JH, Zhao W, Amin N, Arzumanyan Z, Astrup A, Bakker SJL, Baldassarre D, Beekman M, Bergman RN, Bertoni A, Blüher M, Bonnycastle LL, Bornstein SR, Bowden DW, Cai Q, Campbell A, Campbell H, Chang YC, de Geus EJC, Dehghan A, Du S, Eiriksdottir G, Farmaki AE, Frånberg M, Fuchsberger C, Gao Y, Gjesing AP, Goel A, Han S, Hartman CA, Herder C, Hicks AA, Hsieh CH, Hsueh WA, Ichihara S, Igase M, Ikram MA, Johnson WC, Jørgensen ME, Joshi PK, Kalyani RR, Kandeel FR, Katsuya T, Khor CC, Kiess W, Kolcic I, Kuulasmaa T, Kuusisto J, Läll K, Lam K, Lawlor DA, Lee NR, Lemaitre RN, Li H, Lin SY, Lindström J, Linneberg A, Liu J, Lorenzo C, Matsubara T, Matsuda F, Mingrone G, Mooijaart S, Moon S, Nabika T, Nadkarni GN, Nadler JL, Nelis M, Neville MJ, Norris JM, Ohyagi Y, Peters A, Peyser PA, Polasek O, Qi Q, Raven D, Reilly DF, Reiner A, Rivideneira F, Roll K, Rudan I, Sabanayagam C, Sandow K, Sattar N, Schürmann A, Shi J, Stringham HM, Taylor KD, Teslovich TM, Thuesen B, Timmers PRHJ, Tremoli E, Tsai MY, Uitterlinden A, van Dam RM, van Heemst D, van Hylckama Vlieg A, van Vliet-Ostaptchouk JV, Vangipurapu J, Vestergaard H, Wang T, Willems van Dijk K, Zemunik T, Abecasis GR, Adair LS, Aguilar-Salinas CA, Alarcón-Riquelme ME, An P, Aviles-Santa L, Becker DM, Beilin LJ, Bergmann S, Bisgaard H, Black C, Boehnke M, Boerwinkle E, Böhm BO, Bønnelykke K, Boomsma DI, Bottinger EP, Buchanan TA, Canouil M, Caulfield MJ, Chambers JC, Chasman DI, Chen YDI, Cheng CY, Collins FS, Correa A, Cucca F, de Silva HJ, Dedoussis G, Elmståhl S, Evans MK, Ferrannini E, Ferrucci L, Florez JC, Franks PW, Frayling TM, Froguel P, Gigante B, Goodarzi MO, Gordon-Larsen P, Grallert H, Grarup N, Grimsgaard S, Groop L, Gudnason V, Guo X, Hamsten A, Hansen T, Hayward C, Heckbert SR, Horta BL, Huang W, Ingelsson E, James PS, Jarvelin MR, Jonas JB, Jukema JW, Kaleebu P, Kaplan R, Kardia SLR, Kato N, Keinanen-Kiukaanniemi SM, Kim BJ, Kivimaki M, Koistinen HA, Kooner JS, Körner A, Kovacs P, Kuh D, Kumari M, Kutalik Z, Laakso M, Lakka TA, Launer LJ, Leander K, Li H, Lin X, Lind L, Lindgren C, Liu S, Loos RJF, Magnusson PKE, Mahajan A, Metspalu A, Mook-Kanamori DO, Mori TA, Munroe PB, Njølstad I, O'Connell JR, Oldehinkel AJ, Ong KK, Padmanabhan S, Palmer CNA, Palmer ND, Pedersen O, Pennell CE, Porteous DJ, Pramstaller PP, Province MA, Psaty BM, Qi L, Raffel LJ, Rauramaa R, Redline S, Ridker PM, Rosendaal FR, Saaristo TE, Sandhu M, Saramies J, Schneiderman N, Schwarz P, Scott LJ, Selvin E, Sever P, Shu XO, Slagboom PE, Small KS, Smith BH, Snieder H, Sofer T, Sørensen TIA, Spector TD, Stanton A, Steves CJ, Stumvoll M, Sun L, Tabara Y, Tai ES, Timpson NJ, Tönjes A, Tuomilehto J, Tusie T, Uusitupa M, van der Harst P, van Duijn C, Vitart V, Vollenweider P, Vrijkotte TGM, Wagenknecht LE, Walker M, Wang YX, Wareham NJ, Watanabe RM, Watkins H, Wei WB, Wickremasinghe AR, Willemsen G, Wilson JF, Wong TY, Wu JY, Xiang AH, Yanek LR, Yengo L, Yokota M, Zeggini E, Zheng W, Zonderman AB, Rotter JI, Gloyn AL, McCarthy MI, Dupuis J, Meigs JB, Scott RA, Prokopenko I, Leong A, Liu CT, Parker SCJ, Mohlke KL, Langenberg C, Wheeler E, Morris AP, Barroso I. The trans-ancestral genomic architecture of glycemic traits. Nat Genet 2021; 53:840-860. [PMID: 34059833 PMCID: PMC7610958 DOI: 10.1038/s41588-021-00852-9] [Show More Authors] [Citation(s) in RCA: 427] [Impact Index Per Article: 106.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10-8), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.
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Affiliation(s)
- Ji Chen
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Cassandra N Spracklen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA
| | - Gaëlle Marenne
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
- Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, France
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Laura J Corbin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Sara M Willems
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Xiaoshuai Zhang
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Momoko Horikoshi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
| | - Thibaud S Boutin
- Medical Research Council Human Genetics Unit, Institute for Genetics and Molecular Medicine, Edinburgh, UK
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Johannes Waage
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kei Hang Katie Chan
- Department of Epidemiology, Brown University School of Public Health, Brown University, Providence, RI, USA
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong SAR, China
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mila D Anasanti
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Audrey Y Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jani Heikkinen
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jaeyoung Hong
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Shaofeng Huo
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Marika A Kaakinen
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Section of Statistical Multi-omics, Department of Clinical and Experimental Research, University of Surrey, Guildford, UK
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Winfried März
- SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University Graz, Graz, Austria
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, Heidelberg University, Mannheim, Baden-Württemberg, Germany
| | | | - Anne Ndungu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kari E North
- CVD Genetic Epidemiology Computational Laboratory, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | | | - Debashree Ray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rebecca Rohde
- CVD Genetic Epidemiology Computational Laboratory, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Denis Rybin
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- HPI Digital Health Center, Digital Health and Personalized Medicine, Hasso Plattner Institute, Potsdam, Germany
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National Univeristy of Singapore and National University Health System, Singapore, Singapore
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lorraine Southam
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Carol A Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Yujie Wang
- CVD Genetic Epidemiology Computational Laboratory, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Emil V R Appel
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Brody
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Noël P Burtt
- Metabolism Program, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Claudia P Cabrera
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Brian E Cade
- Department of Medicine, Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National Univeristy of Singapore and National University Health System, Singapore, Singapore
| | - Xiaoran Chai
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore, Singapore
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Brian H Chen
- Department of Epidemiology, The Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Kumaraswamy Naidu Chitrala
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yen-Feng Chiu
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Hugoline G de Haan
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Graciela E Delgado
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, Heidelberg University, Mannheim, Baden-Württemberg, Germany
| | - Ayse Demirkan
- Section of Statistical Multi-omics, Department of Clinical and Experimental Research, University of Surrey, Guildford, UK
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jorgen Engmann
- Institute of Cardiovascular Science, University College London, London, UK
| | - Segun A Fatumo
- Uganda Medical Informatics Centre (UMIC), MRC/UVRI and London School of Hygiene & Tropical Medicine (Uganda Research Unit), Entebbe, Uganda
- London School of Hygiene & Tropical Medicine, London, UK
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | | | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jung Ho Gong
- Department of Epidemiology, Brown University School of Public Health, Brown University, Providence, RI, USA
| | - Stefan Gustafsson
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Yang Hai
- Department of Statistics, The University of Auckland, Science Center, Auckland, New Zealand
| | - Fernando P Hartwig
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Jing He
- Department of Medicine, Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yoriko Heianza
- Department of Epidemiology, Tulane University Obesity Research Center, Tulane University, New Orleans, LA, USA
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Alicia Huerta-Chagoya
- Molecular Biology and Genomic Medicine Unit, National Council for Science and Technology, Mexico City, Mexico
- Molecular Biology and Genomic Medicine Unit, National Institute of Medical Sciences and Nutrition, Mexico City, Mexico
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Richard A Jensen
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, Heidelberg University, Mannheim, Baden-Württemberg, Germany
| | - Ishminder K Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
| | - Shuiqing Lai
- Department of Epidemiology, Brown University School of Public Health, Brown University, Providence, RI, USA
| | - Leslie A Lange
- Department of Medicine, Divison of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Marie Lauzon
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Man Li
- Department of Medicine, Division of Nephrology and Hypertension, University of Utah, Salt Lake City, UT, USA
| | - Symen Ligthart
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jun Liu
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Valeriya Lyssenko
- Department of Clinical Science, Center for Diabetes Research, University of Bergen, Bergen, Norway
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmo, Sweden
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Carola Marzi
- Institute of Epidemiology, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - May E Montasser
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Abhishek Nag
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Damia Noce
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Neil R Robertson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Richa Saxena
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Bengt Sennblad
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kazuya Setoh
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Icelandic Heart Association, Kopavogur, Iceland
| | - Thomas Sparsø
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rona J Strawbridge
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Department of Medicine Solna, Cardiovascular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Erik van den Akker
- Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, the Netherlands
- Department of Biomedical Data Sciences, Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Genomics PLC, Oxford, UK
| | - Mandy Vogel
- Center of Pediatric Research, University Children's Hospital Leipzig, University of Leipzig Medical Center, Leipzig, Germany
| | - Heming Wang
- Department of Medicine, Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Nan Wang
- Department of Preventive Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- University of Southern California Diabetes and Obesity Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Helen R Warren
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tom Wilsgaard
- Department of Community Medicine, Faculty of Health Sciences, UIT the Arctic University of Norway, Tromsø, Norway
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Andrew R Wood
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Tian Xie
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mohammad Hadi Zafarmand
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jing-Hua Zhao
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Zorayr Arzumanyan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Arne Astrup
- Department of Nutrition, Exercise, and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Stephan J L Bakker
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Damiano Baldassarre
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
- Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Marian Beekman
- Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Richard N Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alain Bertoni
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Matthias Blüher
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Lori L Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institues of Health, Bethesda, MD, USA
| | - Stefan R Bornstein
- Department for Prevention and Care of Diabetes, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Qiuyin Cai
- Department of Medicine, Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Yi Cheng Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
| | - Eco J C de Geus
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Shufa Du
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | | | - Aliki Eleni Farmaki
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Mattias Frånberg
- Department of Medicine Solna, Cardiovascular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Yutang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Anette P Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anuj Goel
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sohee Han
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Catharina A Hartman
- Department of Psychiatry, Interdisciplinary Center Psychopathy and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Düsseldorf, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Chang-Hsun Hsieh
- Internal Medicine, Endocrine and Metabolism, Tri-Service General Hospital, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Willa A Hsueh
- Internal Medicine, Endocrinology, Diabetes and Metabolism, Diabetes and Metabolism Research Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Michiya Igase
- Department of Anti-aging Medicine, Ehime University Graduate School of Medicine, Toon, Japan
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- National Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Rita R Kalyani
- Department of Medicine, Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fouad R Kandeel
- Clinical Diabetes, Endocrinology and Metabolism, Translational Research and Cellular Therapeutics, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wieland Kiess
- Center of Pediatric Research, University Children's Hospital Leipzig, University of Leipzig Medical Center, Leipzig, Germany
| | - Ivana Kolcic
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Teemu Kuulasmaa
- Institute of Biomedicine, Bioinformatics Center, Univeristy of Eastern Finland, Kuopio, Finland
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kristi Läll
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kelvin Lam
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nanette R Lee
- USC-Office of Population Studies Foundation, University of San Carlos, Cebu City, the Philippines
- Department of Anthropology, Sociology and History, University of San Carlos, Cebu City, the Philippines
| | - Rozenn N Lemaitre
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Honglan Li
- State Key Laboratory of Oncogene and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shih-Yi Lin
- Center for Geriatrics and Gerontology, Taichung Veterans General Hospital, Taichung, Taiwan
- National Defense Medical Center, National Yang-Ming University, Taipei, Taiwan
| | - Jaana Lindström
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Carlos Lorenzo
- Department of Medicine, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Tatsuaki Matsubara
- Department of Internal Medicine, Aichi Gakuin University School of Dentistry, Nagoya, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Geltrude Mingrone
- Department of Diabetes, Diabetes, and Nutritional Sciences, James Black Centre, King's College London, London, UK
| | - Simon Mooijaart
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sanghoon Moon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerry L Nadler
- Department of Medicine and Pharmacology, New York Medical College School of Medicine, Valhalla, NY, USA
| | - Mari Nelis
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jill M Norris
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yasumasa Ohyagi
- Department of Geriatric Medicine and Neurology, Ehime University Graduate School of Medicine, Toon, Japan
| | - Annette Peters
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians University Munich, Munich, Germany
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Ozren Polasek
- Department of Public Health, University of Split School of Medicine, Split, Croatia
- Gen-Info, Zagreb, Croatia
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Dennis Raven
- Department of Psychiatry, Interdisciplinary Center Psychopathy and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dermot F Reilly
- Genetics and Pharmacogenomics, Merck Sharp & Dohme, Kenilworth, NJ, USA
| | - Alex Reiner
- Department of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Fernando Rivideneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Kathryn Roll
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Igor Rudan
- Centre for Global Health, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Charumathi Sabanayagam
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Kevin Sandow
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Naveed Sattar
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Annette Schürmann
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Jinxiu Shi
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Academy of Science & Technology (SAST), Shanghai, China
| | - Heather M Stringham
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Betina Thuesen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National Univeristy of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jana V van Vliet-Ostaptchouk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jagadish Vangipurapu
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Bornholms Hospital, Rønne, Denmark
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Ko Willems van Dijk
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
- Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Tatijana Zemunik
- Department of Human Biology, University of Split School of Medicine, Split, Croatia
| | - Gonçalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Carlos Alberto Aguilar-Salinas
- Department of Endocrinology and Metabolism, Instituto Nacional de Ciencias Medicas y Nutricion, Mexico City, Mexico
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición and Tec Salud, Mexico City, Mexico
- Instituto Tecnológico y de Estudios Superiores de Monterrey Tec Salud, Monterrey, Mexico
| | - Marta E Alarcón-Riquelme
- Department of Medical Genomics, Pfizer/University of Granada/Andalusian Government Center for Genomics and Oncological Research (GENYO), Granada, Spain
- Institute for Environmental Medicine, Chronic Inflammatory Diseases, Karolinska Institutet, Solna, Sweden
| | - Ping An
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA
| | - Larissa Aviles-Santa
- Clinical and Health Services Research, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
| | - Diane M Becker
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence J Beilin
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Perth, Western Australia, Australia
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Corri Black
- Aberdeen Centre for Health Data Science, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Michael Boehnke
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Bernhard O Böhm
- Division of Endocrinology and Diabetes, Graduate School of Molecular Endocrinology and Diabetes, University of Ulm, Ulm, Germany
- LKC School of Medicine, Nanyang Technological University, Singapore and Imperial College London, UK, Singapore, Singapore
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - D I Boomsma
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Digital Health Center, Hasso Plattner Institut, University Potsdam, Potsdam, Germany
| | - Thomas A Buchanan
- University of Southern California Diabetes and Obesity Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Physiology and Neuroscience, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Mickaël Canouil
- INSERM UMR 1283/CNRS UMR 8199, European Institute for Diabetes (EGID), Université de Lille, Lille, France
- INSERM UMR 1283/CNRS UMR 8199, European Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, France
| | - Mark J Caulfield
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ching-Yu Cheng
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Francis S Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institues of Health, Bethesda, MD, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Kallithea, Greece
| | - Sölve Elmståhl
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - Luigi Ferrucci
- Intramural Research Program, National Institute of Aging, Baltimore, MD, USA
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul W Franks
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmo, Sweden
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Timothy M Frayling
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Philippe Froguel
- INSERM UMR 1283/CNRS UMR 8199, European Institute for Diabetes (EGID), Université de Lille, Lille, France
- INSERM UMR 1283/CNRS UMR 8199, European Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, France
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - Bruna Gigante
- Department of Medicine, Cardiovascular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mark O Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Harald Grallert
- Institute of Epidemiology, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sameline Grimsgaard
- Department of Community Medicine, Faculty of Health Sciences, UIT the Arctic University of Norway, Tromsø, Norway
| | - Leif Groop
- Diabetes Centre, Lund University, Lund, Sweden
- Finnish Institute of Molecular Medicine, Helsinki University, Helsinki, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Anders Hamsten
- Department of Medicine Solna, Cardiovascular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan R Heckbert
- Department of Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Bernardo L Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Academy of Science & Technology (SAST), Shanghai, China
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Pankow S James
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Marjo-Ritta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu Univerisity Hospital, OYS, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Institute of Molecular and Clinical Ophthalmology Basel IOB, Basel, Switzerland
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
- Department of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Norihiro Kato
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Sirkka M Keinanen-Kiukaanniemi
- Faculty of Medicine, Institute of Health Sciences, University of Oulu, Oulu, Finland
- Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Heikki A Koistinen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Antje Körner
- Center of Pediatric Research, University Children's Hospital Leipzig, University of Leipzig Medical Center, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Zoltan Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Institute of Primary Care and Public Health, Division of Biostatistics, University of Lausanne, Lausanne, Switzerland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Karin Leander
- Institute of Environmental Medicine, Cardiovascular and Nutritional Epidemiology, Karolinska Institutet, Stockholm, Sweden
| | - Huaixing Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xu Lin
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lars Lind
- Department of Medical Sciences, University of Uppsala, Uppsala, Sweden
| | - Cecilia Lindgren
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Simin Liu
- Department of Epidemiology, Brown University School of Public Health, Brown University, Providence, RI, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics and the Swedish Twin Registry, Karolinska Institutet, Stockholm, Sweden
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Trevor A Mori
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Perth, Western Australia, Australia
| | - Patricia B Munroe
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Inger Njølstad
- Department of Community Medicine, Faculty of Health Sciences, UIT the Arctic University of Norway, Tromsø, Norway
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Albertine J Oldehinkel
- Department of Psychiatry, Interdisciplinary Center Psychopathy and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | | | - Michael A Province
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA
| | - Bruce M Psaty
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Health Services, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Lu Qi
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Leslie J Raffel
- Department of Pediatrics, Genetic and Genomic Medicine, University of California, Irvine, Irvine, CA, USA
| | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Susan Redline
- Department of Medicine, Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Havard Medical School, Boston, MA, USA
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Timo E Saaristo
- Tampere, Finnish Diabetes Association, Tampere, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | | | | | | | - Peter Schwarz
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Department for Prevention and Care of Diabetes, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich, University Hospital and Faculty of Medicine, Dresden, Germany
| | - Laura J Scott
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - P Eline Slagboom
- Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Alice Stanton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael Stumvoll
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Liang Sun
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National Univeristy of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Cardiovascular and Metabolic Disease Signature Research Program, Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Anke Tönjes
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Saudi Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Teresa Tusie
- Molecular Biology and Genomic Medicine Unit, National Institute of Medical Sciences and Nutrition, Mexico City, Mexico
- Department of Genomic Medicine and Environmental Toxicology, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico
| | - Matti Uusitupa
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Pim van der Harst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Tanja G M Vrijkotte
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Lynne E Wagenknecht
- Department of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Mark Walker
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ya X Wang
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Nick J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Richard M Watanabe
- Department of Preventive Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- University of Southern California Diabetes and Obesity Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Physiology and Neuroscience, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Hugh Watkins
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Wen B Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | | | - Gonneke Willemsen
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Tien-Yin Wong
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Anny H Xiang
- Department of Research and Evaluation, Kaiser Permanente of Southern California, Pasadena, CA, USA
| | - Lisa R Yanek
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Loïc Yengo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Inga Prokopenko
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Section of Statistical Multi-omics, Department of Clinical and Experimental Research, University of Surrey, Guildford, UK
| | - Aaron Leong
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Diabetes Unit and Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Eleanor Wheeler
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
- Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Inês Barroso
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK.
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
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Hu Y, Stilp AM, McHugh CP, Rao S, Jain D, Zheng X, Lane J, Méric de Bellefon S, Raffield LM, Chen MH, Yanek LR, Wheeler M, Yao Y, Ren C, Broome J, Moon JY, de Vries PS, Hobbs BD, Sun Q, Surendran P, Brody JA, Blackwell TW, Choquet H, Ryan K, Duggirala R, Heard-Costa N, Wang Z, Chami N, Preuss MH, Min N, Ekunwe L, Lange LA, Cushman M, Faraday N, Curran JE, Almasy L, Kundu K, Smith AV, Gabriel S, Rotter JI, Fornage M, Lloyd-Jones DM, Vasan RS, Smith NL, North KE, Boerwinkle E, Becker LC, Lewis JP, Abecasis GR, Hou L, O'Connell JR, Morrison AC, Beaty TH, Kaplan R, Correa A, Blangero J, Jorgenson E, Psaty BM, Kooperberg C, Walton RT, Kleinstiver BP, Tang H, Loos RJF, Soranzo N, Butterworth AS, Nickerson D, Rich SS, Mitchell BD, Johnson AD, Auer PL, Li Y, Mathias RA, Lettre G, Pankratz N, Laurie CC, Laurie CA, Bauer DE, Conomos MP, Reiner AP. Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:874-893. [PMID: 33887194 DOI: 10.1016/j.ajhg.2021.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Whole-genome sequencing (WGS), a powerful tool for detecting novel coding and non-coding disease-causing variants, has largely been applied to clinical diagnosis of inherited disorders. Here we leveraged WGS data in up to 62,653 ethnically diverse participants from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and assessed statistical association of variants with seven red blood cell (RBC) quantitative traits. We discovered 14 single variant-RBC trait associations at 12 genomic loci, which have not been reported previously. Several of the RBC trait-variant associations (RPN1, ELL2, MIDN, HBB, HBA1, PIEZO1, and G6PD) were replicated in independent GWAS datasets imputed to the TOPMed reference panel. Most of these discovered variants are rare/low frequency, and several are observed disproportionately among non-European Ancestry (African, Hispanic/Latino, or East Asian) populations. We identified a 3 bp indel p.Lys2169del (g.88717175_88717177TCT[4]) (common only in the Ashkenazi Jewish population) of PIEZO1, a gene responsible for the Mendelian red cell disorder hereditary xerocytosis (MIM: 194380), associated with higher mean corpuscular hemoglobin concentration (MCHC). In stepwise conditional analysis and in gene-based rare variant aggregated association analysis, we identified several of the variants in HBB, HBA1, TMPRSS6, and G6PD that represent the carrier state for known coding, promoter, or splice site loss-of-function variants that cause inherited RBC disorders. Finally, we applied base and nuclease editing to demonstrate that the sentinel variant rs112097551 (nearest gene RPN1) acts through a cis-regulatory element that exerts long-range control of the gene RUVBL1 which is essential for hematopoiesis. Together, these results demonstrate the utility of WGS in ethnically diverse population-based samples and gene editing for expanding knowledge of the genetic architecture of quantitative hematologic traits and suggest a continuum between complex trait and Mendelian red cell disorders.
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Affiliation(s)
- Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98105, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | | | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Nancy Heard-Costa
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mary Cushman
- Department of Medicine, Larner College of Medicine at the University of Vermont, Burlington, VT 05405, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia and Department of Genetics University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | | | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | | | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98105, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98105, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Lifang Hou
- Northwestern University, Chicago, IL 60208, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Terri H Beaty
- School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98105, USA
| | - Russell T Walton
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Soranzo
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Department of Human Genetics, Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Debbie Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53205, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA 21205, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, QC H1T 1C8, Canada
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA.
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13
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Sun P, Zhou W, Fu Y, Cheung CYY, Dong Y, Yang ML, Zhang H, Jia J, Huo Y, Willer CJ, Chen YE, Tang CS, Tse HF, Lam KSL, Gao W, Xu M, Yu H, Sham PC, Zhang Y, Ganesh SK. An Asian-specific MPL genetic variant alters JAK-STAT signaling and influences platelet count in the population. Hum Mol Genet 2021; 30:836-842. [PMID: 33693786 DOI: 10.1093/hmg/ddab062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 12/27/2022] Open
Abstract
Genomic discovery efforts for hematological traits have been successfully conducted through genome-wide association study on samples of predominantly European ancestry. We sought to conduct unbiased genetic discovery for coding variants that influence hematological traits in a Han Chinese population. A total of 5257 Han Chinese subjects from Beijing, China were included in the discovery cohort and analyzed by an Illumina ExomeChip array. Replication analyses were conducted in 3827 independent Chinese subjects. We analyzed 12 hematological traits and identified 22 exome-wide significant single-nucleotide polymorphisms (SNP)-trait associations with 15 independent SNPs. Our study provides replication for two associations previously reported but not replicated. Further, one association was identified and replicated in the current study, of a coding variant in the myeloproliferative leukemia (MPL) gene, c.793C > T, p.Leu265Phe (L265F) with increased platelet count (β = 20.6 109 cells/l, Pmeta-analysis = 2.6 × 10-13). This variant is observed at ~2% population frequency in East Asians, whereas it has not been reported in gnomAD European or African populations. Functional analysis demonstrated that expression of MPL L265F in Ba/F3 cells resulted in enhanced phosphorylation of Stat3 and ERK1/2 as compared with the reference MPL allele, supporting altered activation of the JAK-STAT signal transduction pathway as the mechanism underlying the novel association between MPL L265F and platelet count.
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Affiliation(s)
- Pengfei Sun
- Department of Cardiology, Peking University First Hospital, Beijing 100034, China
| | - Wei Zhou
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi Fu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing 100191, China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing 100191, China
| | - Chloe Y Y Cheung
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong 999077, China
| | - Yujun Dong
- Department of Hematology, Peking University First Hospital, Beijing 100034, China
| | - Min-Lee Yang
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - He Zhang
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jia Jia
- Department of Cardiology, Peking University First Hospital, Beijing 100034, China
| | - Yong Huo
- Department of Cardiology, Peking University First Hospital, Beijing 100034, China
| | - Cristen J Willer
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Y Eugene Chen
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Clara S Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong 999077, China
| | - Hung-Fat Tse
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Karen S L Lam
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Wei Gao
- Department of Cardiology, Peking University Third Hospital, Beijing 100083, China
| | - Ming Xu
- Department of Cardiology, Peking University Third Hospital, Beijing 100083, China
| | - Haiyi Yu
- Department of Cardiology, Peking University Third Hospital, Beijing 100083, China
| | - Pak Chung Sham
- Department of Psychiatry and Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong 999077, China
| | - Yan Zhang
- Department of Cardiology, Peking University First Hospital, Beijing 100034, China.,Institute of Cardiovascular Disease?Peking University First Hospital, Beijing, 100034, China
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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14
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The Role, Function, and Mechanism of Long Intergenic Noncoding RNA1184 (linc01184) in Colorectal Cancer. DISEASE MARKERS 2021; 2021:8897906. [PMID: 33564344 PMCID: PMC7867457 DOI: 10.1155/2021/8897906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/21/2021] [Indexed: 01/07/2023]
Abstract
Background Long intergenic noncoding RNA1184 (linc01184) has been recently discovered; however, its role in human diseases is limited to date. The present study is aimed at investigating the expression pattern and mechanism of linc01184 in colorectal cancer (CRC) tumorigenesis. Methods The expression of linc01184 in CRC tissues and cell lines was compared with that in normal controls. The functions of linc01184 in CRC cells were identified by overexpression and small interfering RNA (siRNA) approaches in vitro. Meanwhile, the target gene prediction software, luciferase reporter, RNA pull-down, and western blotting assays were used to analyze the oncogenic mechanism. Results We found that linc01184 was obviously upregulated in CRC tissues and cells when compared to normal controls, and its upregulation had a positive association with the CRC progression. linc01184 knockdown significantly suppressed CRC cell proliferation and invasion and promoted apoptosis. Besides, linc01184 acted as a competitive endogenous RNA (ceRNA) by directly binding to microRNA-331 (miR-331), and its overexpression resulted in notable increases of human epidermal growth factor receptor 2 (HER2), phosphorylated Ser/Thr kinases (p-Akt), and extracellular regulated protein kinase 1/2 (p-ERK1/2) at posttranscriptional levels in CRC cells, which were antagonized by miR-331. Conclusions The findings reveal for the first time that linc01184 is an enhancer for the proliferation and invasion of CRC by functioning as a ceRNA through the linc01184-miR-331-HER2-p-Akt/ERK1/2 pathway regulatory network.
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15
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The genetic structure and adaptation of Andean highlanders and Amazonians are influenced by the interplay between geography and culture. Proc Natl Acad Sci U S A 2020; 117:32557-32565. [PMID: 33277433 DOI: 10.1073/pnas.2013773117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Western South America was one of the worldwide cradles of civilization. The well-known Inca Empire was the tip of the iceberg of an evolutionary process that started 11,000 to 14,000 years ago. Genetic data from 18 Peruvian populations reveal the following: 1) The between-population homogenization of the central southern Andes and its differentiation with respect to Amazonian populations of similar latitudes do not extend northward. Instead, longitudinal gene flow between the northern coast of Peru, Andes, and Amazonia accompanied cultural and socioeconomic interactions revealed by archeology. This pattern recapitulates the environmental and cultural differentiation between the fertile north, where altitudes are lower, and the arid south, where the Andes are higher, acting as a genetic barrier between the sharply different environments of the Andes and Amazonia. 2) The genetic homogenization between the populations of the arid Andes is not only due to migrations during the Inca Empire or the subsequent colonial period. It started at least during the earlier expansion of the Wari Empire (600 to 1,000 years before present). 3) This demographic history allowed for cases of positive natural selection in the high and arid Andes vs. the low Amazon tropical forest: in the Andes, a putative enhancer in HAND2-AS1 (heart and neural crest derivatives expressed 2 antisense RNA1, a noncoding gene related to cardiovascular function) and rs269868-C/Ser1067 in DUOX2 (dual oxidase 2, related to thyroid function and innate immunity) genes and, in the Amazon, the gene encoding for the CD45 protein, essential for antigen recognition by T and B lymphocytes in viral-host interaction.
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16
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Population-Matched Transcriptome Prediction Increases TWAS Discovery and Replication Rate. iScience 2020; 23:101850. [PMID: 33313492 PMCID: PMC7721644 DOI: 10.1016/j.isci.2020.101850] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Most genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) focus on European populations; however, these results cannot always be accurately applied to non-European populations due to genetic architecture differences. Using GWAS summary statistics in the Population Architecture using Genomics and Epidemiology study, which comprises ∼50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we perform TWAS to determine gene-trait associations. We compared results using three transcriptome prediction models derived from Multi-Ethnic Study of Atherosclerosis populations: the African American and Hispanic/Latino (AFHI) model, the European (EUR) model, and the African American, Hispanic/Latino, and European (ALL) model. We identified 240 unique significant trait-associated genes. We found more significant, colocalized genes that replicate in larger cohorts when applying the AFHI model than the EUR or ALL model. Thus, TWAS with population-matched transcriptome models have more power for discovery and replication, demonstrating the need for more transcriptome studies in diverse populations. TWAS mechanistically extends GWAS findings in diverse populations Population-matched transcriptome models detect more replicable associations Colocalization shows GWAS variants likely act through gene expression regulation More GWAS and transcriptome modeling in diverse populations are needed
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17
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Heterogeneous phenotype of Hereditary Xerocytosis in association with PIEZO1 variants. Blood Cells Mol Dis 2020; 82:102413. [DOI: 10.1016/j.bcmd.2020.102413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 02/02/2023]
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18
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Hodonsky CJ, Baldassari AR, Bien SA, Raffield LM, Highland HM, Sitlani CM, Wojcik GL, Tao R, Graff M, Tang W, Thyagarajan B, Buyske S, Fornage M, Hindorff LA, Li Y, Lin D, Reiner AP, North KE, Loos RJF, Kooperberg C, Avery CL. Ancestry-specific associations identified in genome-wide combined-phenotype study of red blood cell traits emphasize benefits of diversity in genomics. BMC Genomics 2020; 21:228. [PMID: 32171239 PMCID: PMC7071748 DOI: 10.1186/s12864-020-6626-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Quantitative red blood cell (RBC) traits are highly polygenic clinically relevant traits, with approximately 500 reported GWAS loci. The majority of RBC trait GWAS have been performed in European- or East Asian-ancestry populations, despite evidence that rare or ancestry-specific variation contributes substantially to RBC trait heritability. Recently developed combined-phenotype methods which leverage genetic trait correlation to improve statistical power have not yet been applied to these traits. Here we leveraged correlation of seven quantitative RBC traits in performing a combined-phenotype analysis in a multi-ethnic study population. RESULTS We used the adaptive sum of powered scores (aSPU) test to assess combined-phenotype associations between ~ 21 million SNPs and seven RBC traits in a multi-ethnic population (maximum n = 67,885 participants; 24% African American, 30% Hispanic/Latino, and 43% European American; 76% female). Thirty-nine loci in our multi-ethnic population contained at least one significant association signal (p < 5E-9), with lead SNPs at nine loci significantly associated with three or more RBC traits. A majority of the lead SNPs were common (MAF > 5%) across all ancestral populations. Nineteen additional independent association signals were identified at seven known loci (HFE, KIT, HBS1L/MYB, CITED2/FILNC1, ABO, HBA1/2, and PLIN4/5). For example, the HBA1/2 locus contained 14 conditionally independent association signals, 11 of which were previously unreported and are specific to African and Amerindian ancestries. One variant in this region was common in all ancestries, but exhibited a narrower LD block in African Americans than European Americans or Hispanics/Latinos. GTEx eQTL analysis of all independent lead SNPs yielded 31 significant associations in relevant tissues, over half of which were not at the gene immediately proximal to the lead SNP. CONCLUSION This work identified seven loci containing multiple independent association signals for RBC traits using a combined-phenotype approach, which may improve discovery in genetically correlated traits. Highly complex genetic architecture at the HBA1/2 locus was only revealed by the inclusion of African Americans and Hispanics/Latinos, underscoring the continued importance of expanding large GWAS to include ancestrally diverse populations.
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Affiliation(s)
- Chani J. Hodonsky
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
- University of Virginia Center for Public Health Genomics, 1355 Lee St, Charlottesville, VA 22908 USA
| | - Antoine R. Baldassari
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Stephanie A. Bien
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599 USA
| | - Heather M. Highland
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Colleen M. Sitlani
- University of Washington, 1730 Minor Ave, Ste 1360, Seattle, WA 98101 USA
| | - Genevieve L. Wojcik
- Stanford University School of Medicine, 291 Campus Dr, Stanford, CA 94305 USA
| | - Ran Tao
- Vanderbilt University, 2525 West End Ave #1100, Nashville, TN 37203 USA
| | - Marielisa Graff
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Weihong Tang
- University of Minnesota, 420 Delaware St SE, Minneapolis, MN 55455 USA
| | | | - Steve Buyske
- Rutgers University, 683 Hoes Ln W, Piscataway, NJ 08854 USA
| | - Myriam Fornage
- University of Texas Houston, 7000 Fannin Street, Houston, TX 77030 USA
| | - Lucia A. Hindorff
- National Human Genome Research Institute, 31 Center Dr, Bethesda, MD 20894 USA
| | - Yun Li
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Danyu Lin
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
| | - Alex P. Reiner
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109 USA
- University of Washington, 1705 NE Pacific St, Seattle, WA 98195 USA
| | - Kari E. North
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599 USA
| | - Ruth J. F. Loos
- Icahn School of Medicine at Mount Sinai, 1468 Madison Ave, New York, NY 10029 USA
| | | | - Christy L. Avery
- University of North Carolina Gillings School of Public Health, 135 Dauer Dr, Chapel Hill, NC 27599 USA
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19
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Lin SH, Loftfield E, Sampson JN, Zhou W, Yeager M, Freedman ND, Chanock SJ, Machiela MJ. Mosaic chromosome Y loss is associated with alterations in blood cell counts in UK Biobank men. Sci Rep 2020; 10:3655. [PMID: 32108144 PMCID: PMC7046668 DOI: 10.1038/s41598-020-59963-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/04/2020] [Indexed: 12/31/2022] Open
Abstract
Mosaic loss of Y chromosome (mLOY) is the most frequently detected somatic copy number alteration in leukocytes of men. In this study, we investigate blood cell counts as a potential mechanism linking mLOY to disease risk in 206,353 UK males. Associations between mLOY, detected by genotyping arrays, and blood cell counts were assessed by multivariable linear models adjusted for relevant risk factors. Among the participants, mLOY was detected in 39,809 men. We observed associations between mLOY and reduced erythrocyte count (−0.009 [−0.014, −0.005] × 1012 cells/L, p = 2.75 × 10−5) and elevated thrombocyte count (5.523 [4.862, 6.183] × 109 cells/L, p = 2.32 × 10−60) and leukocyte count (0.218 [0.198, 0.239] × 109 cells/L, p = 9.22 × 10−95), particularly for neutrophil count (0.174 × [0.158, 0.190]109 cells/L, p = 1.24 × 10−99) and monocyte count (0.021 [0.018 to 0.024] × 109 cells/L, p = 6.93 × 10−57), but lymphocyte count was less consistent (0.016 [0.007, 0.025] × 109 cells/L, p = 8.52 × 10−4). Stratified analyses indicate these associations are independent of the effects of aging and smoking. Our findings provide population-based evidence for associations between mLOY and blood cell counts that should stimulate investigation of the underlying biological mechanisms linking mLOY to cancer and chronic disease risk.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Erikka Loftfield
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Josh N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 8717 Grovemont Circle, Gaithersburg, MD, 20877, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 8717 Grovemont Circle, Gaithersburg, MD, 20877, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.
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20
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Kowalski MH, Qian H, Hou Z, Rosen JD, Tapia AL, Shan Y, Jain D, Argos M, Arnett DK, Avery C, Barnes KC, Becker LC, Bien SA, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Buyske S, Cai J, Cho MH, Choi SH, Choquet H, Cupples LA, Cushman M, Daya M, de Vries PS, Ellinor PT, Faraday N, Fornage M, Gabriel S, Ganesh SK, Graff M, Gupta N, He J, Heckbert SR, Hidalgo B, Hodonsky CJ, Irvin MR, Johnson AD, Jorgenson E, Kaplan R, Kardia SLR, Kelly TN, Kooperberg C, Lasky-Su JA, Loos RJF, Lubitz SA, Mathias RA, McHugh CP, Montgomery C, Moon JY, Morrison AC, Palmer ND, Pankratz N, Papanicolaou GJ, Peralta JM, Peyser PA, Rich SS, Rotter JI, Silverman EK, Smith JA, Smith NL, Taylor KD, Thornton TA, Tiwari HK, Tracy RP, Wang T, Weiss ST, Weng LC, Wiggins KL, Wilson JG, Yanek LR, Zöllner S, North KE, Auer PL, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Hematology & Hemostasis Working Group, Raffield LM, Reiner AP, Li Y. Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations. PLoS Genet 2019; 15:e1008500. [PMID: 31869403 PMCID: PMC6953885 DOI: 10.1371/journal.pgen.1008500] [Citation(s) in RCA: 187] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 01/10/2020] [Accepted: 10/30/2019] [Indexed: 01/10/2023] Open
Abstract
Most genome-wide association and fine-mapping studies to date have been conducted in individuals of European descent, and genetic studies of populations of Hispanic/Latino and African ancestry are limited. In addition, these populations have more complex linkage disequilibrium structure. In order to better define the genetic architecture of these understudied populations, we leveraged >100,000 phased sequences available from deep-coverage whole genome sequencing through the multi-ethnic NHLBI Trans-Omics for Precision Medicine (TOPMed) program to impute genotypes into admixed African and Hispanic/Latino samples with genome-wide genotyping array data. We demonstrated that using TOPMed sequencing data as the imputation reference panel improves genotype imputation quality in these populations, which subsequently enhanced gene-mapping power for complex traits. For rare variants with minor allele frequency (MAF) < 0.5%, we observed a 2.3- to 6.1-fold increase in the number of well-imputed variants, with 11-34% improvement in average imputation quality, compared to the state-of-the-art 1000 Genomes Project Phase 3 and Haplotype Reference Consortium reference panels. Impressively, even for extremely rare variants with minor allele count <10 (including singletons) in the imputation target samples, average information content rescued was >86%. Subsequent association analyses of TOPMed reference panel-imputed genotype data with hematological traits (hemoglobin (HGB), hematocrit (HCT), and white blood cell count (WBC)) in ~21,600 African-ancestry and ~21,700 Hispanic/Latino individuals identified associations with two rare variants in the HBB gene (rs33930165 with higher WBC [p = 8.8x10-15] in African populations, rs11549407 with lower HGB [p = 1.5x10-12] and HCT [p = 8.8x10-10] in Hispanics/Latinos). By comparison, neither variant would have been genome-wide significant if either 1000 Genomes Project Phase 3 or Haplotype Reference Consortium reference panels had been used for imputation. Our findings highlight the utility of the TOPMed imputation reference panel for identification of novel rare variant associations not previously detected in similarly sized genome-wide studies of under-represented African and Hispanic/Latino populations.
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Affiliation(s)
- Madeline H. Kowalski
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Huijun Qian
- Department of Statistics and Operation Research, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ziyi Hou
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan D. Rosen
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Amanda L. Tapia
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Yue Shan
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Maria Argos
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Donna K. Arnett
- College of Public Health, University of Kentucky, Lexington, Kentucky, United States of America
| | - Christy Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kathleen C. Barnes
- Department of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Lewis C. Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Stephanie A. Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, Texas, United States of America
| | - Eric Boerwinkle
- Human Genome Sequencing Center, University of Texas Health Science Center at Houston; Baylor College of Medicine, Houston, Texas, United States of America
- 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, Texas, United States of America
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Steve Buyske
- Department of Statistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Jianwen Cai
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Seung Hoan Choi
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, California, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Mary Cushman
- Departments of Medicine & Pathology, Larner College of Medicine, University of Vermont, Colchester, Vermont, United States of America
| | - Michelle Daya
- Department of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Patrick T. Ellinor
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Nauder Faraday
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Myriam Fornage
- School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Stacey Gabriel
- Genomics Platform, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Santhi K. Ganesh
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Misa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Namrata Gupta
- Genomics Platform, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, Los Angeles, United States of America
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, Washington, United States of America
| | - Bertha Hidalgo
- Department of Epidemiology, Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chani J. Hodonsky
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Andrew D. Johnson
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, Massachusetts, United States of America
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California, United States of America
| | - Robert Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanika N. Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, Los Angeles, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jessica A. Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Steven A. Lubitz
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Rasika A. Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Caitlin P. McHugh
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Courtney Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Jee-Young Moon
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - George J. Papanicolaou
- National Heart, Lung, and Blood Institute, Division of Cardiovascular Sciences, PPSP/EB, NIH, Bethesda, Maryland, United States of America
| | - Juan M. Peralta
- Department of Human Genetics and South Texas Diabetes Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, Texas, United States of America
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - 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, California, United States of America
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, Washington, United States of America
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, Washington, United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Hemant K. Tiwari
- Department of Biostatistics, Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Russell P. Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larrner College of Medicine, University of Vermont, Colchester, Vermont, United States of America
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lu-Chen Weng
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Lisa R. Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Sebastian Zöllner
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center of Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paul L. Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | | | | | - Laura M. Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Alexander P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, United States of America
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21
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Sarnowski C, Leong A, Raffield LM, Wu P, de Vries PS, DiCorpo D, Guo X, Xu H, Liu Y, Zheng X, Hu Y, Brody JA, Goodarzi MO, Hidalgo BA, Highland HM, Jain D, Liu CT, Naik RP, O'Connell JR, Perry JA, Porneala BC, Selvin E, Wessel J, Psaty BM, Curran JE, Peralta JM, Blangero J, Kooperberg C, Mathias R, Johnson AD, Reiner AP, Mitchell BD, Cupples LA, Vasan RS, Correa A, Morrison AC, Boerwinkle E, Rotter JI, Rich SS, Manning AK, Dupuis J, Meigs JB. Impact of Rare and Common Genetic Variants on Diabetes Diagnosis by Hemoglobin A1c in Multi-Ancestry Cohorts: The Trans-Omics for Precision Medicine Program. Am J Hum Genet 2019; 105:706-718. [PMID: 31564435 DOI: 10.1016/j.ajhg.2019.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/20/2019] [Indexed: 01/21/2023] Open
Abstract
Hemoglobin A1c (HbA1c) is widely used to diagnose diabetes and assess glycemic control in individuals with diabetes. However, nonglycemic determinants, including genetic variation, may influence how accurately HbA1c reflects underlying glycemia. Analyzing the NHLBI Trans-Omics for Precision Medicine (TOPMed) sequence data in 10,338 individuals from five studies and four ancestries (6,158 Europeans, 3,123 African-Americans, 650 Hispanics, and 407 East Asians), we confirmed five regions associated with HbA1c (GCK in Europeans and African-Americans, HK1 in Europeans and Hispanics, FN3K and/or FN3KRP in Europeans, and G6PD in African-Americans and Hispanics) and we identified an African-ancestry-specific low-frequency variant (rs1039215 in HBG2 and HBE1, minor allele frequency (MAF) = 0.03). The most associated G6PD variant (rs1050828-T, p.Val98Met, MAF = 12% in African-Americans, MAF = 2% in Hispanics) lowered HbA1c (-0.88% in hemizygous males, -0.34% in heterozygous females) and explained 23% of HbA1c variance in African-Americans and 4% in Hispanics. Additionally, we identified a rare distinct G6PD coding variant (rs76723693, p.Leu353Pro, MAF = 0.5%; -0.98% in hemizygous males, -0.46% in heterozygous females) and detected significant association with HbA1c when aggregating rare missense variants in G6PD. We observed similar magnitude and direction of effects for rs1039215 (HBG2) and rs76723693 (G6PD) in the two largest TOPMed African American cohorts, and we replicated the rs76723693 association in the UK Biobank African-ancestry participants. These variants in G6PD and HBG2 were monomorphic in the European and Asian samples. African or Hispanic ancestry individuals carrying G6PD variants may be underdiagnosed for diabetes when screened with HbA1c. Thus, assessment of these variants should be considered for incorporation into precision medicine approaches for diabetes diagnosis.
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Affiliation(s)
- Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA.
| | - Aaron Leong
- Division of General Internal Medicine, Massachusetts General Hospital, Boston 02114, MA USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Daniel DiCorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, LABioMed and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Yao Hu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98108, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Bertha A Hidalgo
- University of Alabama at Birmingham, Department of Epidemiology, Birmingham, AL 35294, USA
| | - Heather M Highland
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Rakhi P Naik
- Division of Hematology, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - James A Perry
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Bianca C Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Boston 02114, MA USA
| | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jennifer Wessel
- Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202, USA; Department of Medicine and Diabetes Translational Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, USA; Departments of Epidemiology and Health Services, University of Washington, Seattle, WA 98195, 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 78520, 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 78520, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98108, USA
| | - Rasika Mathias
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; GeneSTAR Research Program, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute and Boston University's Framingham Heart Study, Framingham MA 01702, USA; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98108, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute and Boston University's Framingham Heart Study, Framingham MA 01702, USA
| | - Ramachandran S Vasan
- National Heart, Lung, and Blood Institute and Boston University's Framingham Heart Study, Framingham MA 01702, USA; Section of Preventive Medicine and Epidemiology, Evans Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Whitaker Cardiovascular Institute and Cardiology Section, Evans Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adolfo Correa
- Departments of Medicine, Pediatrics, and Population Health Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; The Jackson Heart Study, Jackson, MS 39213, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, LABioMed and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Alisa K Manning
- Division of General Internal Medicine, Massachusetts General Hospital, Boston 02114, MA USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute and Boston University's Framingham Heart Study, Framingham MA 01702, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston 02114, MA USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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22
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Moon JY, Louie TL, Jain D, Sofer T, Schurmann C, Below JE, Lai CQ, Aviles-Santa ML, Talavera GA, Smith CE, Petty LE, Bottinger EP, Chen YDI, Taylor KD, Daviglus ML, Cai J, Wang T, Tucker KL, Ordovás JM, Hanis CL, Loos RJF, Schneiderman N, Rotter JI, Kaplan RC, Qi Q. A Genome-Wide Association Study Identifies Blood Disorder-Related Variants Influencing Hemoglobin A 1c With Implications for Glycemic Status in U.S. Hispanics/Latinos. Diabetes Care 2019; 42:1784-1791. [PMID: 31213470 PMCID: PMC6702612 DOI: 10.2337/dc19-0168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/24/2019] [Indexed: 02/03/2023]
Abstract
OBJECTIVE We aimed to identify hemoglobin A1c (HbA1c)-associated genetic variants and examine their implications for glycemic status evaluated by HbA1c in U.S. Hispanics/Latinos with diverse genetic ancestries. RESEARCH DESIGN AND METHODS We conducted a genome-wide association study (GWAS) of HbA1c in 9,636 U.S. Hispanics/Latinos without diabetes from the Hispanic Community Health Study/Study of Latinos, followed by a replication among 4,729 U.S. Hispanics/Latinos from three independent studies. RESULTS Our GWAS and replication analyses showed 10 previously known and novel loci associated with HbA1c at genome-wide significance levels (P < 5.0 × 10-8). In particular, two African ancestry-specific variants, HBB-rs334 and G6PD-rs1050828, which are causal mutations for sickle cell disease and G6PD deficiency, respectively, had ∼10 times larger effect sizes on HbA1c levels (β = -0.31% [-3.4 mmol/mol]) and -0.35% [-3.8 mmol/mol] per minor allele, respectively) compared with other HbA1c-associated variants (0.03-0.04% [0.3-0.4 mmol/mol] per allele). A novel Amerindian ancestry-specific variant, HBM-rs145546625, was associated with HbA1c and hematologic traits but not with fasting glucose. The prevalence of hyperglycemia (prediabetes and diabetes) defined using fasting glucose or oral glucose tolerance test 2-h glucose was similar between carriers of HBB-rs334 or G6PD-rs1050828 HbA1c-lowering alleles and noncarriers, whereas the prevalence of hyperglycemia defined using HbA1c was significantly lower in carriers than in noncarriers (12.2% vs. 28.4%, P < 0.001). After recalibration of the HbA1c level taking HBB-rs334 and G6PD-rs1050828 into account, the prevalence of hyperglycemia in carriers was similar to noncarriers (31.3% vs. 28.4%, P = 0.28). CONCLUSIONS This study in U.S. Hispanics/Latinos found several ancestry-specific alleles associated with HbA1c through erythrocyte-related rather than glycemic-related pathways. The potential influences of these nonglycemic-related variants need to be considered when the HbA1c test is performed.
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Affiliation(s)
- Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| | - Tin L Louie
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jennifer E Below
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | - Chao-Qiang Lai
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | | | - Gregory A Talavera
- Graduate School of Public Health, San Diego State University, San Diego, CA
| | - Caren E Smith
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | - Lauren E Petty
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | - Erwin P Bottinger
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, CA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, CA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL
| | - Jianwen Cai
- Department of Biostatistics and Collaborative Studies Coordinating Center, University of North Carolina, Chapel Hill, NC
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| | - Katherine L Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA
| | - José M Ordovás
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA
- IMDEA Food Institute, Campus de Excelencia Internacional Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Craig L Hanis
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Harbor-UCLA Medical Center, Torrance, CA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
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23
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Abstract
Risk of disease is multifactorial and can be shaped by socio-economic, demographic, cultural, environmental and genetic factors. Our understanding of the genetic determinants of disease risk has greatly advanced with the advent of genome-wide association studies (GWAS), which detect associations between genetic variants and complex traits or diseases by comparing populations of cases and controls. However, much of this discovery has occurred through GWAS of individuals of European ancestry, with limited representation of other populations, including from Africa, The Americas, Asia and Oceania. Population demography, genetic drift and adaptation to environments over thousands of years have led globally to the diversification of populations. This global genomic diversity can provide new opportunities for discovery and translation into therapies, as well as a better understanding of population disease risk. Large-scale multi-ethnic and representative biobanks and population health resources provide unprecedented opportunities to understand the genetic determinants of disease on a global scale.
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24
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Thayer TE, Huang S, Levinson RT, Farber-Eger E, Assad TR, Huston JH, Mosley JD, Wells QS, Brittain EL. Unbiased Phenome-Wide Association Studies of Red Cell Distribution Width Identifies Key Associations with Pulmonary Hypertension. Ann Am Thorac Soc 2019; 16:589-598. [PMID: 30608875 PMCID: PMC6491061 DOI: 10.1513/annalsats.201809-594oc] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/03/2019] [Indexed: 12/27/2022] Open
Abstract
Rationale: Red cell distribution width (RDW) is a prognostic factor in many diseases; however, its clinical utility remains limited because the relative value of RDW as a biomarker across disease states has not been established. Objectives: To establish an unbiased RDW disease hierarchy to guide the clinical use of RDW and to assess its relationship to cardiovascular hemodynamic and structural parameters. Methods: We performed phenome-wide association studies for RDW in discovery and replication cohorts derived from a deidentified electronic health record in nonanemic individuals. RDW values obtained within 30 days of echocardiogram or right heart catheterization were tested for association with structural and hemodynamic variables. Results: RDW was associated with 263 phenotypes in both men and women in the discovery cohort (n = 121,530), 48 of which replicated in an independent cohort (n = 2,039). The strongest associations were observed with pulmonary arterial hypertension (odds ratio [OR], 2.1; 95% confidence interval [CI], 1.9-2.3), chronic pulmonary heart disease (OR, 2.0; 95% CI, 1.9-2.2), and congestive heart failure (OR, 1.9; 95% CI, 1.8-2.0); P < 1 × 10-74 for all. By echocardiography, RDW was higher in the setting of right ventricular dysfunction than left ventricular dysfunction (P < 0.001). Measured invasively, mean pulmonary arterial pressure was associated with RDW (21 vs. 33 mm Hg at 25th vs. 75th percentile RDW; P < 1 × 10-7) and remained strongly significant even when controlling for mean pulmonary capillary wedge pressure (21 vs. 29 mm Hg at 25th vs. 75th percentile RDW; P < 1 × 10-7). Conclusions: Among 1,364 coded medical conditions, increased RDW was strongly associated with pulmonary hypertension and heart failure. Hemodynamic and echocardiographic phenotyping confirmed these associations and underscored that the most clinically relevant phenotype associated with RDW was pulmonary hypertension. These hypothesis-generating findings highlight the potential shared pathophysiology of pulmonary hypertension and elevated RDW. Elevated RDW in the absence of anemia should alert clinicians to the potential for underlying cardiopulmonary disease.
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Affiliation(s)
| | - Shi Huang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
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Fatumo S, Carstensen T, Nashiru O, Gurdasani D, Sandhu M, Kaleebu P. Complimentary Methods for Multivariate Genome-Wide Association Study Identify New Susceptibility Genes for Blood Cell Traits. Front Genet 2019; 10:334. [PMID: 31080455 PMCID: PMC6497788 DOI: 10.3389/fgene.2019.00334] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/28/2019] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have found hundreds of novel loci associated with full blood count (FBC) phenotypes. However, most of these studies were performed in a single phenotype framework without putting into consideration the clinical relatedness among traits. In this work, in addition to the standard univariate GWAS, we also use two different multivariate methods to perform the first multiple traits GWAS of FBC traits in ∼7000 individuals from the Ugandan General Population Cohort (GPC). We started by performing the standard univariate GWAS approach. We then performed our first multivariate method, in this approach, we tested for marker associations with 15 FBC traits simultaneously in a multivariate mixed model implemented in GEMMA while accounting for the relatedness of individuals and pedigree structures, as well as population substructure. In this analysis, we provide a framework for the combination of multiple phenotypes in multivariate GWAS analysis and show evidence of multi-collinearity whenever the correlation between traits exceeds the correlation coefficient threshold of r 2 >=0.75. This approach identifies two known and one novel loci. In the second multivariate method, we applied principal component analysis (PCA) to the same 15 correlated FBC traits. We then tested for marker associations with each PC in univariate linear mixed models implemented in GEMMA. We show that the FBC composite phenotype as assessed by each PC expresses information that is not completely encapsulated by the individual FBC traits, as this approach identifies three known and five novel loci that were not identified using both the standard univariate and multivariate GWAS methods. Across both multivariate methods, we identified six novel loci. As a proof of concept, both multivariate methods also identified known loci, HBB and ITFG3. The two multivariate methods show that multivariate genotype-phenotype methods increase power and identify novel genotype-phenotype associations not found with the standard univariate GWAS in the same dataset.
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Affiliation(s)
- Segun Fatumo
- Uganda Medical Informatics Centre, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda,London School of Hygiene and Tropical Medicine, London, United Kingdom,H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria,*Correspondence: Segun Fatumo, ;
| | - Tommy Carstensen
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Oyekanmi Nashiru
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Deepti Gurdasani
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Manjinder Sandhu
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom,Division of Computational Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Pontiano Kaleebu
- Uganda Medical Informatics Centre, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda,London School of Hygiene and Tropical Medicine, London, United Kingdom
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Varicose veins of lower extremities: Insights from the first large-scale genetic study. PLoS Genet 2019; 15:e1008110. [PMID: 30998689 PMCID: PMC6490943 DOI: 10.1371/journal.pgen.1008110] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/30/2019] [Accepted: 03/25/2019] [Indexed: 11/19/2022] Open
Abstract
Varicose veins of lower extremities (VVs) are a common multifactorial vascular disease. Genetic factors underlying VVs development remain largely unknown. Here we report the first large-scale study of VVs performed on a freely available genetic data of 408,455 European-ancestry individuals. We identified the 12 reliably associated loci that explain 13% of the SNP-based heritability, and prioritized the most likely causal genes CASZ1, PIEZO1, PPP3R1, EBF1, STIM2, HFE, GATA2, NFATC2, and SOX9. VVs-associated variants within these loci exhibited pleiotropic effects on several phenotypes including blood pressure/hypertension and blood cell traits. Gene set enrichment analysis revealed gene categories related to abnormal vasculogenesis. Genetic correlation analysis confirmed known epidemiological associations between VVs and deep venous thrombosis, weight, rough labor, and standing job, and found a genetic overlap with multiple traits that have not been previously suspected to share common genetic background with VVs. These traits included educational attainment, fluid intelligence and prospective memory scores, walking pace (negative correlation with VVs), smoking, height, number of operations, pain, and gonarthrosis (positive correlation with VVs). Finally, Mendelian randomization analysis provided evidence for causal effects of plasma levels of MICB and CD209 proteins, and anthropometric traits such as waist and hip circumference, height, weight, and both fat and fat-free mass. Our results provide novel insight into both VVs genetics and etiology. The revealed genes and proteins can be considered as good candidates for follow-up functional studies and might be of interest as potential drug targets. Varicose veins of lower extremities (VVs) affect about 30% of adults in developed countries and cause both cosmetic and health problems. A strong body of evidence indicates that heredity plays an important role in the etiology of this condition. However, genetic basis of VVs remains poorly understood. Here, we present the results of the first large-scale genetic study for VVs. We identified genes which are the most likely involved in VVs pathogenesis. We show that VVs are correlated at a genetic level with numerous traits and phenotypes, including those already known from prior epidemiological studies (deep venous thrombosis, body mass index, standing job, etc.) as well as with those that have not been suspected to share common genetic background with VVs (fluid intelligence and prospective memory scores, smoking, walking pace, pain all over the body, and other traits). Finally, using genetic variants as instruments, we demonstrate direct causal effects of the traits related to anthropometry, such as height and weight, and plasma levels of immune-related proteins MICB and CD209. Our study provides novel insight into both VVs genetics and etiology. The revealed genes (CASZ1, PIEZO1, PPP3R1, EBF1, STIM2, HFE, GATA2, NFATC2, and SOX9) and proteins (MICB and CD209) can be considered as good candidates for follow-up functional studies and might be of interest as potential drug targets.
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Bien SA, Wojcik GL, Hodonsky CJ, Gignoux CR, Cheng I, Matise TC, Peters U, Kenny EE, North KE. The Future of Genomic Studies Must Be Globally Representative: Perspectives from PAGE. Annu Rev Genomics Hum Genet 2019; 20:181-200. [PMID: 30978304 DOI: 10.1146/annurev-genom-091416-035517] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past decade has seen a technological revolution in human genetics that has empowered population-level investigations into genetic associations with phenotypes. Although these discoveries rely on genetic variation across individuals, association studies have overwhelmingly been performed in populations of European descent. In this review, we describe limitations faced by single-population studies and provide an overview of strategies to improve global representation in existing data sets and future human genomics research via diversity-focused, multiethnic studies. We highlight the successes of individual studies and meta-analysis consortia that have provided unique knowledge. Additionally, we outline the approach taken by the Population Architecture Using Genomics and Epidemiology (PAGE) study to develop best practices for performing genetic epidemiology in multiethnic contexts. Finally, we discuss how limiting investigations to single populations impairs findings in the clinical domain for both rare-variant identification and genetic risk prediction.
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Affiliation(s)
- Stephanie A Bien
- Department of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; ,
| | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; ,
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado 80045, USA;
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94158, USA;
| | - Tara C Matise
- Department of Genetics, Rutgers University, New Brunswick, New Jersey 08554, USA;
| | - Ulrike Peters
- Department of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; ,
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; ,
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Gouveia MH, Bergen AW, Borda V, Nunes K, Leal TP, Ogwang MD, Yeboah ED, Mensah JE, Kinyera T, Otim I, Nabalende H, Legason ID, Mpoloka SW, Mokone GG, Kerchan P, Bhatia K, Reynolds SJ, Birtwum RB, Adjei AA, Tettey Y, Tay E, Hoover R, Pfeiffer RM, Biggar RJ, Goedert JJ, Prokunina-Olsson L, Dean M, Yeager M, Lima-Costa MF, Hsing AW, Tishkoff SA, Chanock SJ, Tarazona-Santos E, Mbulaiteye SM. Genetic signatures of gene flow and malaria-driven natural selection in sub-Saharan populations of the "endemic Burkitt Lymphoma belt". PLoS Genet 2019; 15:e1008027. [PMID: 30849090 PMCID: PMC6426263 DOI: 10.1371/journal.pgen.1008027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 03/20/2019] [Accepted: 02/17/2019] [Indexed: 12/13/2022] Open
Abstract
Populations in sub-Saharan Africa have historically been exposed to intense selection from chronic infection with falciparum malaria. Interestingly, populations with the highest malaria intensity can be identified by the increased occurrence of endemic Burkitt Lymphoma (eBL), a pediatric cancer that affects populations with intense malaria exposure, in the so called "eBL belt" in sub-Saharan Africa. However, the effects of intense malaria exposure and sub-Saharan populations' genetic histories remain poorly explored. To determine if historical migrations and intense malaria exposure have shaped the genetic composition of the eBL belt populations, we genotyped ~4.3 million SNPs in 1,708 individuals from Ghana and Northern Uganda, located on opposite sides of eBL belt and with ≥ 7 months/year of intense malaria exposure and published evidence of high incidence of BL. Among 35 Ghanaian tribes, we showed a predominantly West-Central African ancestry and genomic footprints of gene flow from Gambian and East African populations. In Uganda, the North West population showed a predominantly Nilotic ancestry, and the North Central population was a mixture of Nilotic and Southern Bantu ancestry, while the Southwest Ugandan population showed a predominant Southern Bantu ancestry. Our results support the hypothesis of diverse ancestral origins of the Ugandan, Kenyan and Tanzanian Great Lakes African populations, reflecting a confluence of Nilotic, Cushitic and Bantu migrations in the last 3000 years. Natural selection analyses suggest, for the first time, a strong positive selection signal in the ATP2B4 gene (rs10900588) in Northern Ugandan populations. These findings provide important baseline genomic data to facilitate disease association studies, including of eBL, in eBL belt populations.
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Affiliation(s)
- Mateus H. Gouveia
- Instituto de Pesquisa René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Center for Research on Genomics & Global Health, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Andrew W. Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Victor Borda
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Thiago P. Leal
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Statistics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Martin D. Ogwang
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | | | | | - Tobias Kinyera
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Isaac Otim
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | | | | | | | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, University of Botswana School of Medicine, Gaborone, Botswana
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Steven J. Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | | | | | - Yao Tettey
- University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- University of Ghana Medical School, Accra, Ghana
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Robert J. Biggar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - James J. Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, US Department of Health and Human Services, Frederick, Maryland, United States of America
| | - M. Fernanda Lima-Costa
- Instituto de Pesquisa René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Ann W. Hsing
- Stanford Cancer Institute, Stanford University, Stanford, California, United States of America
| | - Sarah A. Tishkoff
- Department of Genetics and Biology, University of Pennsylvania, Philadelphia, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sam M. Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
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29
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Grinde KE, Qi Q, Thornton TA, Liu S, Shadyab AH, Chan KHK, Reiner AP, Sofer T. Generalizing polygenic risk scores from Europeans to Hispanics/Latinos. Genet Epidemiol 2019; 43:50-62. [PMID: 30368908 PMCID: PMC6330129 DOI: 10.1002/gepi.22166] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/12/2018] [Accepted: 08/28/2018] [Indexed: 12/17/2022]
Abstract
Polygenic risk scores (PRSs) are weighted sums of risk allele counts of single-nucleotide polymorphisms (SNPs) associated with a disease or trait. PRSs are typically constructed based on published results from Genome-Wide Association Studies (GWASs), and the majority of which has been performed in large populations of European ancestry (EA) individuals. Although many genotype-trait associations have generalized across populations, the optimal choice of SNPs and weights for PRSs may differ between populations due to different linkage disequilibrium (LD) and allele frequency patterns. We compare various approaches for PRS construction, using GWAS results from both large EA studies and a smaller study in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos (HCHS/SOL, n = 12 , 803 ). We consider multiple approaches for selecting SNPs and for computing SNP weights. We study the performance of the resulting PRSs in an independent study of Hispanics/Latinos from the Women's Health Initiative (WHI, n = 3 , 582 ). We support our investigation with simulation studies of potential genetic architectures in a single locus. We observed that selecting variants based on EA GWASs generally performs well, except for blood pressure trait. However, the use of EA GWASs for weight estimation was suboptimal. Using non-EA GWAS results to estimate weights improved results.
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Affiliation(s)
- Kelsey E. Grinde
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Simin Liu
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Aladdin H. Shadyab
- Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA, USA
| | - Kei Hang K. Chan
- Department of Epidemiology, Brown University, Providence, RI, USA
- Departments of Biomedical Sciences and Electronic Engineering, City University of Hong Kong, HKSAR
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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30
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Reiner AP, Johnson AD. Platelet Genomics. Platelets 2019. [DOI: 10.1016/b978-0-12-813456-6.00005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Soares-Souza G, Borda V, Kehdy F, Tarazona-Santos E. Admixture, Genetics and Complex Diseases in Latin Americans and US Hispanics. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0151-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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32
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Jeong C, Witonsky DB, Basnyat B, Neupane M, Beall CM, Childs G, Craig SR, Novembre J, Di Rienzo A. Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal. PLoS Genet 2018; 14:e1007650. [PMID: 30188897 PMCID: PMC6143271 DOI: 10.1371/journal.pgen.1007650] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/18/2018] [Accepted: 08/21/2018] [Indexed: 12/21/2022] Open
Abstract
Adaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. The results of genome-wide association analyses and tests for polygenic adaptations showed evidence of positive selection for alleles associated with more pregnancies and live births and evidence of negative selection for those associated with higher offspring mortality. Lower hemoglobin level did not show clear evidence for polygenic adaptation, despite its strong association with an EPAS1 haplotype carrying selective sweep signals.
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Affiliation(s)
- Choongwon Jeong
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - David B. Witonsky
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Hospital, Kathmandu, Nepal
| | | | - Cynthia M. Beall
- Department of Anthropology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Geoff Childs
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Sienna R. Craig
- Department of Anthropology, Dartmouth College, Hanover, New Hampshire, United States of America
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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33
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Jo Hodonsky C, Schurmann C, Schick UM, Kocarnik J, Tao R, van Rooij FJ, Wassel C, Buyske S, Fornage M, Hindorff LA, Floyd JS, Ganesh SK, Lin DY, North KE, Reiner AP, Loos RJ, Kooperberg C, Avery CL. Generalization and fine mapping of red blood cell trait genetic associations to multi-ethnic populations: The PAGE Study. Am J Hematol 2018; 93:10.1002/ajh.25161. [PMID: 29905378 PMCID: PMC6300146 DOI: 10.1002/ajh.25161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Red blood cell (RBC) traits provide insight into a wide range of physiological states and exhibit moderate to high heritability, making them excellent candidates for genetic studies to inform underlying biologic mechanisms. Previous RBC trait genome-wide association studies were performed primarily in European- or Asian-ancestry populations, missing opportunities to inform understanding of RBC genetic architecture in diverse populations and reduce intervals surrounding putative functional SNPs through fine-mapping. Here, we report the first fine-mapping of six correlated (Pearson's r range: |0.04 - 0.92|) RBC traits in up to 19,036 African Americans and 19,562 Hispanic/Latinos participants of the Population Architecture using Genomics and Epidemiology (PAGE) consortium. Trans-ethnic meta-analysis of race/ethnic- and study-specific estimates for approximately 11,000 SNPs flanking 13 previously identified association signals as well as 150,000 additional array-wide SNPs was performed using inverse-variance meta-analysis after adjusting for study and clinical covariates. Approximately half of previously reported index SNP-RBC trait associations generalized to the trans-ethnic study population (p<1.7x10-4 ); previously unreported independent association signals within the ABO region reinforce the potential for multiple functional variants affecting the same locus. Trans-ethnic fine-mapping did not reveal additional signals at the HFE locus independent of the known functional variants. Finally, we identified a potential novel association in the Hispanic/Latino study population at the HECTD4/RPL6 locus for RBC count (p=1.9x10-7 ). The identification of a previously unknown association, generalization of a large proportion of known association signals, and refinement of known association signals all exemplify the benefits of genetic studies in diverse populations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chani Jo Hodonsky
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jonathan Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Frank Ja van Rooij
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000, the Netherlands
| | - Christina Wassel
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT
| | - Steve Buyske
- Department of Statistics and Biostatistics, Hill Center, Rutgers, The State University of New Jersey, 110 Frelinghuysen Rd. Piscataway, NY
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National institutes of Health, Bethesda, MD
| | - James S Floyd
- Departments of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Santhi K Ganesh
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
| | - Dan-Yu Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
| | - Kari E North
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Ruth Jf Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC
- Carolina Population Center, University of North Carolina, Chapel Hill, NC
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34
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Verma A, Lucas A, Verma SS, Zhang Y, Josyula N, Khan A, Hartzel DN, Lavage DR, Leader J, Ritchie MD, Pendergrass SA. PheWAS and Beyond: The Landscape of Associations with Medical Diagnoses and Clinical Measures across 38,662 Individuals from Geisinger. Am J Hum Genet 2018; 102:592-608. [PMID: 29606303 PMCID: PMC5985339 DOI: 10.1016/j.ajhg.2018.02.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/20/2018] [Indexed: 01/23/2023] Open
Abstract
Most phenome-wide association studies (PheWASs) to date have used a small to moderate number of SNPs for association with phenotypic data. We performed a large-scale single-cohort PheWAS, using electronic health record (EHR)-derived case-control status for 541 diagnoses using International Classification of Disease version 9 (ICD-9) codes and 25 median clinical laboratory measures. We calculated associations between these diagnoses and traits with ∼630,000 common frequency SNPs with minor allele frequency > 0.01 for 38,662 individuals. In this landscape PheWAS, we explored results within diseases and traits, comparing results to those previously reported in genome-wide association studies (GWASs), as well as previously published PheWASs. We further leveraged the context of functional impact from protein-coding to regulatory regions, providing a deeper interpretation of these associations. The comprehensive nature of this PheWAS allows for novel hypothesis generation, the identification of phenotypes for further study for future phenotypic algorithm development, and identification of cross-phenotype associations.
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Affiliation(s)
- Anurag Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Anastasia Lucas
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shefali S Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yu Zhang
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Navya Josyula
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Anqa Khan
- Mount Holyoke College, South Hadley, MA 01075, USA
| | - Dustin N Hartzel
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Daniel R Lavage
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Joseph Leader
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah A Pendergrass
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA.
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Raffield LM, Ulirsch JC, Naik RP, Lessard S, Handsaker RE, Jain D, Kang HM, Pankratz N, Auer PL, Bao EL, Smith JD, Lange LA, Lange EM, Li Y, Thornton TA, Young BA, Abecasis GR, Laurie CC, Nickerson DA, McCarroll SA, Correa A, Wilson JG, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Hematology & Hemostasis, Diabetes, and Structural Variation TOPMed Working Groups, Lettre G, Sankaran VG, Reiner AP. Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease. PLoS Genet 2018; 14:e1007293. [PMID: 29590102 PMCID: PMC5891078 DOI: 10.1371/journal.pgen.1007293] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/09/2018] [Accepted: 03/06/2018] [Indexed: 11/18/2022] Open
Abstract
Co-inheritance of α-thalassemia has a significant protective effect on the severity of complications of sickle cell disease (SCD), including stroke. However, little information exists on the association and interactions for the common African ancestral α-thalassemia mutation (-α3.7 deletion) and β-globin traits (HbS trait [SCT] and HbC trait) on important clinical phenotypes such as red blood cell parameters, anemia, and chronic kidney disease (CKD). In a community-based cohort of 2,916 African Americans from the Jackson Heart Study, we confirmed the expected associations between SCT, HbC trait, and the -α3.7 deletion with lower mean corpuscular volume/mean corpuscular hemoglobin and higher red blood cell count and red cell distribution width. In addition to the recently recognized association of SCT with lower estimated glomerular filtration rate and glycated hemoglobin (HbA1c), we observed a novel association of the -α3.7 deletion with higher HbA1c levels. Co-inheritance of each additional copy of the -α3.7 deletion significantly lowered the risk of anemia and chronic kidney disease among individuals with SCT (P-interaction = 0.031 and 0.019, respectively). Furthermore, co-inheritance of a novel α-globin regulatory variant was associated with normalization of red cell parameters in individuals with the -α3.7 deletion and significantly negated the protective effect of α-thalassemia on stroke in 1,139 patients with sickle cell anemia from the Cooperative Study of Sickle Cell Disease (CSSCD) (P-interaction = 0.0049). Functional assays determined that rs11865131, located in the major alpha-globin enhancer MCS-R2, was the most likely causal variant. These findings suggest that common α- and β-globin variants interact to influence hematologic and clinical phenotypes in African Americans, with potential implications for risk-stratification and counseling of individuals with SCD and SCT.
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Affiliation(s)
- Laura M. Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jacob C. Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Rakhi P. Naik
- Hematology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Samuel Lessard
- Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
- Montreal Heart Institute, Montréal, Quebec, Canada
| | - Robert E. Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Hyun M. Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nathan Pankratz
- Department of Laboratory Medicine & Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Paul L. Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Erik L. Bao
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Ethan M. Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Bessie A. Young
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Epidemiologic Research and Information Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington, United States of America
| | - Goncalo R. Abecasis
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Steven A. McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | | | - Guillaume Lettre
- Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
- Montreal Heart Institute, Montréal, Quebec, Canada
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (APR); (VGS)
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (APR); (VGS)
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Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham F, Hindorff LA, MacArthur JAL. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol 2018; 19:21. [PMID: 29448949 PMCID: PMC5815218 DOI: 10.1186/s13059-018-1396-2] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022] Open
Abstract
The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations. It is our hope that widespread adoption of this framework will lead to improved analysis, interpretation, and integration of human genomics data.
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Affiliation(s)
- Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Danielle Welter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Emily H. Bowler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Maria Cerezo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Laura W. Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Aoife C. McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Peggy Hall
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-9305 USA
| | - Heather A. Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-9305 USA
| | - Annalisa Milano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Emma Hastings
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Cinzia Malangone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Annalisa Buniello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-9305 USA
| | - Jacqueline A. L. MacArthur
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
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37
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Novel mechanisms of PIEZO1 dysfunction in hereditary xerocytosis. Blood 2017; 130:1845-1856. [PMID: 28716860 DOI: 10.1182/blood-2017-05-786004] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/06/2017] [Indexed: 11/20/2022] Open
Abstract
Mutations in PIEZO1 are the primary cause of hereditary xerocytosis, a clinically heterogeneous, dominantly inherited disorder of erythrocyte dehydration. We used next-generation sequencing-based techniques to identify PIEZO1 mutations in individuals from 9 kindreds referred with suspected hereditary xerocytosis (HX) and/or undiagnosed congenital hemolytic anemia. Mutations were primarily found in the highly conserved, COOH-terminal pore-region domain. Several mutations were novel and demonstrated ethnic specificity. We characterized these mutations using genomic-, bioinformatic-, cell biology-, and physiology-based functional assays. For these studies, we created a novel, cell-based in vivo system for study of wild-type and variant PIEZO1 membrane protein expression, trafficking, and electrophysiology in a rigorous manner. Previous reports have indicated HX-associated PIEZO1 variants exhibit a partial gain-of-function phenotype with generation of mechanically activated currents that inactivate more slowly than wild type, indicating that increased cation permeability may lead to dehydration of PIEZO1-mutant HX erythrocytes. In addition to delayed channel inactivation, we found additional alterations in mutant PIEZO1 channel kinetics, differences in response to osmotic stress, and altered membrane protein trafficking, predicting variant alleles that worsen or ameliorate erythrocyte hydration. These results extend the genetic heterogeneity observed in HX and indicate that various pathophysiologic mechanisms contribute to the HX phenotype.
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