ArticleGenetic epidemiology2019
The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype.
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Article in Genetic epidemiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 6 of them syntheses that pooled it.
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59citing papers in PubMed, 6 pooled it
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Who cites it
59 citing papers in PubMed, 6 syntheses or guidelines pooled it.
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- Mendelian randomization analysis of plasma levels of CD209 and MICB proteins and the risk of varicose veins of lower extremities.PloS one · 2022Pooled it
- Pleiotropy in the Genetic Predisposition to Rheumatoid Arthritis: A Phenome-Wide Association Study and Inverse Variance-Weighted Meta-Analysis.Arthritis & rheumatology (Hoboken, N.J.) · 2020Pooled it
- Minority-centric meta-analyses of blood lipid levels identify novel loci in the Population Architecture using Genomics and Epidemiology (PAGE) study.PLoS genetics · 2020Pooled it
- Genome-wide association studies of missing metabolite measures from two population-based studies.Genome biology · 2026Article
- GWAS analysis of a depression cohort defined by an EHR-phenotyping algorithm reveals the role of immune regulations in depression risk.Frontiers in genetics · 2026Article
- Phenome-wide association study identifies multiple traits associated with a polygenic risk score for colorectal cancer.Human genomics · 2025Article
- Genetic relationships between systemic lupus erythematosus and a positive antinuclear antibody test in the absence of autoimmune disease.Lupus science & medicine · 2025Article
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- Polygenic scores and their applications in kidney disease.Nature reviews. Nephrology · 2025Review
- Constructing a multi-ancestry polygenic risk score for uterine fibroids using publicly available data highlights need for inclusive genetic research.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2025Article
- Unraveling the Immune Signature of Herpes Zoster: Insights Into the Pathophysiology and Human Leukocyte Antigen Risk Profile.The Journal of infectious diseases · 2024Article
- Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction.Nature genetics · 2024Article
- Variant level heritability estimates of type 2 diabetes in African Americans.Scientific reports · 2024Article
- Polygenic Risk for Type 2 Diabetes in African Americans.Diabetes · 2024Article
- Multi-Ancestry Polygenic Risk Score for Coronary Heart Disease Based on an Ancestrally Diverse Genome-Wide Association Study and Population-Specific Optimization.Circulation. Genomic and precision medicine · 2024Article
- A new test for trait mean and variance detects unreported loci for blood-pressure variation.American journal of human genetics · 2024Article
- Clinical associations with a polygenic predisposition to benign lower white blood cell counts.Nature communications · 2024Article
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Authors and funding
41 authors.
Ian B StanawayDepartment of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington.ORCID 0000-0002-0783-0918
Taryn O HallDepartment of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington.
Elisabeth A RosenthalDivision of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington.
Melody PalmerDivision of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington.
Vivek NaranbhaiDepartment of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington.
Rachel KnevelHarvard Medical School, Harvard University, Cambridge, Massachusetts.
Bahram Namjou-KhalesDepartment of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
Robert J CarrollDepartments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee.
Krzysztof KirylukDepartment of Medicine, Columbia University, New York City, New York.
Adam S GordonDivision of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington.
Jodell LinderVanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee.
Kayla Marie HowellVanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee.
Brandy M MapesVanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee.
Frederick T J LinFeinberg School of Medicine, Northwestern University, Chicago, Illinois.
Yoonjung Yoonie JooFeinberg School of Medicine, Northwestern University, Chicago, Illinois.
M Geoffrey HayesFeinberg School of Medicine, Northwestern University, Chicago, Illinois.
Ali G GharaviDepartment of Medicine, Columbia University, New York City, New York.
Sarah A PendergrassGeisinger Research, Rockville, Marland.
Marylyn D RitchieDepartment of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania.
Mariza de AndradeMayo Clinic, Rochester, Minnesota.
Damien C Croteau-ChonkaHarvard Medical School, Harvard University, Cambridge, Massachusetts.
Soumya RaychaudhuriHarvard Medical School, Harvard University, Cambridge, Massachusetts.
Scott T WeissHarvard Medical School, Harvard University, Cambridge, Massachusetts.
Matt LeboHarvard Medical School, Harvard University, Cambridge, Massachusetts.
Sami S AmrHarvard Medical School, Harvard University, Cambridge, Massachusetts.
David CarrellKaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, Washington.
Eric B LarsonKaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, Washington.
Christopher G ChuteSchools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, Maryland.
Laura Jarmila Rasmussen-TorvikFeinberg School of Medicine, Northwestern University, Chicago, Illinois.
Megan J Roy-PuckelwartzFeinberg School of Medicine, Northwestern University, Chicago, Illinois.
Patrick SleimanChildren's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Hakon HakonarsonChildren's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Rongling LiNational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.
Elizabeth W KarlsonDepartment of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania.
Josh F PetersonDepartments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee.
Iftikhar J KulloMayo Clinic, Rochester, Minnesota.
Rex ChisholmFeinberg School of Medicine, Northwestern University, Chicago, Illinois.
Joshua Charles DennyDepartments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee.
Gail P JarvikDivision of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington.
eMERGE NetworkNational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.
David R CrosslinDepartment of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington.
Funding
Northwestern University Clinical and Translational Science Institute (NUCATS)UL1TR001422 · NCATS · NORTHWESTERN UNIVERSITY AT CHICAGO · PI D'AQUILA, RICHARD · 2015 to 2023
$56.8MJH/CIDR Genotyping for Genome-Wide Association StudiesU01HG004438 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 2007 to 2011
$24.2MA Center for GEI Association StudiesU01HG004424 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY · 2007 to 2010
$21.4MUniversity of Washington Biomedical Informatics and Data Science Research Training ProgramT15LM007442 · NLM · UNIVERSITY OF WASHINGTON · PI JOHN H. GENNARI, Andrea L. Hartzler · 2002 to 2026
$19.6MGenomic Basis of Susceptibility to COVID-19 Infection and its ComplicationsU01HG006379 · NHGRI · MAYO CLINIC ROCHESTER · PI Richard R. Sharp · 2011 to 2026
$16.5MFinding Genomic Profiles of COVID-19 Phenotypes from the EHRU01HG008685 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI ELIZABETH W KARLSON, Matthew S Lebo · 2015 to 2026
$13.6MVariation, Function, and Disease Supplement ProgramU01HG008657 · NHGRI · UNIVERSITY OF WASHINGTON · PI David Russell Crosslin, Gail Pairitz Jarvik · 2015 to 2026
$13.4MOMOP information model for eMERGE phenotypingU01HG008680 · NHGRI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Wendy K Chung, GEORGE M HRIPCSAK · 2015 to 2026
$13.3MDNA Sequencing Support for the eMERGE NetworkU01HG008664 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2015 to 2019
$10.9MJoint Biology Consortium Resource-based CenterP30AR070253 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Peter A Nigrovic, Jeffrey Andrew Sparks · 2016 to 2026
$9.4MGlobal Alliance for Genomic Health (GA4GH)U01HG008676 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI LENNON, NIALL JOHN, REHM, HEIDI L · 2015 to 2019
$8.6MThe Electronic Medical Records and Genomics (eMERGE) Network Phase III Coordinating Center (U01)U01HG008701 · NHGRI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI PETERSON, JOSEPH F. · 2015 to 2019
$7.1MNCATS NIH HHS UL1 TR001422NHGRI NIH HHS U01 HG004424NHGRI NIH HHS U01 HG004438NHGRI NIH HHS U01 HG006375NHGRI NIH HHS U01 HG006378NHGRI NIH HHS U01 HG006379NHGRI NIH HHS U01 HG006380NHGRI NIH HHS U01 HG006382NHGRI NIH HHS U01 HG006385NHGRI NIH HHS U01 HG006388NHGRI NIH HHS U01 HG006389NHGRI NIH HHS U01 HG006828NHGRI NIH HHS U01 HG006830NHGRI NIH HHS U01 HG008657NHGRI NIH HHS U01 HG008664NHGRI NIH HHS U01 HG008666NHGRI NIH HHS U01 HG008672NHGRI NIH HHS U01 HG008673NHGRI NIH HHS U01 HG008676NHGRI NIH HHS U01 HG008679NHGRI NIH HHS U01 HG008680NHGRI NIH HHS U01 HG008684NHGRI NIH HHS U01 HG008685NHGRI NIH HHS U01 HG008701NHGRI NIH HHS U01HG8657 (Kaiser Washington/University of Washington), U01HG8685 (Brigham and Women's Hospital), U01HG8672 (Vanderbilt University Medical Center), U01HG8666 (Cincinnati Children's Hospital Medical Center), U01HG6379 (Mayo Clinic), U01HG8679 (Geisinger Clinic), U01HG8680 (Columbia University Health Sciences), U01HG8684 (Children s Hospital of Philadelphia), U01HG8673 (Northwestern University), U01HG8701 (Vanderbilt University Medical Center serving as the Coordinating Center), U01HG8676 (Partners Healthcare/Broad Institute), and U01HG8664 (Baylor College of Medicine), U01HG006828 (Cincinnati Children's Hospital Medical Center/Boston Children's Hospital), U01HG006830 (Children's Hospital of Philadelphia), U01HG006389 (Essentia Institute of Rural Health, Marshfield Clinic Research Foundation and Pennsylvania State University), U01HG006382 (Geisinger Clinic), U01HG006375 (Group Health Cooperative/University of Washington), U01HG006379 (Mayo Clinic), U01HG006380 (Icahn School of Medicine at Mount Sinai), U01HG006388 (Northwestern University), U01HG006378 (Vanderbilt University Medical Center), and U01HG006385 (Vanderbilt University Medical Center serving as the Coordinating Center), U01HG004438 (CIDR), U01HG004424 (the Broad Institute)NHLBI NIH HHS K01 HL127265NIAMS NIH HHS P30 AR070253NLM NIH HHS T15 LM007442
Abstract
The Electronic Medical Records and Genomics (eMERGE) network is a network of medical centers with electronic medical records linked to existing biorepository samples for genomic discovery and genomic medicine research. The network sought to unify the genetic results from 78 Illumina and Affymetrix genotype array batches from 12 contributing medical centers for joint association analysis of 83,717 human participants. In this report, we describe the imputation of eMERGE results and methods to create the unified imputed merged set of genome-wide variant genotype data. We imputed the data using the Michigan Imputation Server, which provides a missing single-nucleotide variant genotype imputation service using the minimac3 imputation algorithm with the Haplotype Reference Consortium genotype reference set. We describe the quality control and filtering steps used in the generation of this data set and suggest generalizable quality thresholds for imputation and phenotype association studies. To test the merged imputed genotype set, we replicated a previously reported chromosome 6 HLA-B herpes zoster (shingles) association and discovered a novel zoster-associated loci in an epigenetic binding site near the terminus of chromosome 3 (3p29).
Indexed as
Electronic Health RecordsGenetic Predisposition to DiseaseGenome-Wide Association StudyAlgorithmsBlack PeopleChromosomes, HumanFemaleHaplotypesHerpes ZosterHomozygoteHumansMalePhenotypePolymorphism, Single NucleotidePrincipal Component AnalysisWhite Peopleelectronic medical recordsgenotypesGWASherpes zostervariants
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