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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
medicine
The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype
Genetic Epidemiology, Volume 43, No. 1, Year 2019
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Description
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). © 2018 The Authors. Genetic Epidemiology Published by Wiley Periodicals, Inc.
Authors & Co-Authors
Rosenthal, Elisabeth A.
United States, Seattle
University of Washington
Naranbhai, Vivek
United States, Seattle
University of Washington
United States, Cambridge
Harvard University
Namjou, Bahram
United States, Cincinnati
Cincinnati Children's Hospital Medical Center
Carroll, Robert J.
United States, Nashville
Vanderbilt University
Kiryluk, Krzysztof
United States, New York
Columbia University
Gordon, Adam S.
United States, Seattle
University of Washington
Lin, Frederick T.J.
United States, Evanston
Northwestern University
Joo, Yoonjung Yoonie
United States, Evanston
Northwestern University
Hayes, Matthew Geoffrey
United States, Evanston
Northwestern University
Gharavi, Ali G.
United States, New York
Columbia University
Pendergrass, Sarah A.
Unknown Affiliation
Ritchie, Marylyn D.
United States, Philadelphia
University of Pennsylvania
de Andrade, Mariza A.
United States, Rochester
Mayo Clinic
Raychaudhuri, Soumya
United States, Cambridge
Harvard University
Weiss, Scott T.
United States, Cambridge
Harvard University
Amr, Sami S.
United States, Cambridge
Harvard University
Carrell, David S.
United States, Seattle
Group Health Cooperative
Larson, Eric B.
United States, Seattle
Group Health Cooperative
Chute, Christopher G.
United States, Baltimore
Johns Hopkins University
Rasmussen-Torvik, Laura J.
United States, Evanston
Northwestern University
Sleiman, Patrick M.A.
United States, Philadelphia
The Children's Hospital of Philadelphia
Håkonarson, Håkon H.
United States, Philadelphia
The Children's Hospital of Philadelphia
Li, Rongling
United States, Bethesda
National Institutes of Health Nih
Karlson, Elizabeth W.
United States, Philadelphia
University of Pennsylvania
Kullo, Iftikhar J.
United States, Rochester
Mayo Clinic
Chisholm, Rex L.
United States, Evanston
Northwestern University
Denny, Joshua C.
United States, Nashville
Vanderbilt University
Jarvik, Gail P.
United States, Seattle
University of Washington
Crosslin, David R.
United States, Seattle
University of Washington
Statistics
Citations: 44
Authors: 29
Affiliations: 12
Identifiers
Doi:
10.1002/gepi.22167
ISSN:
07410395
Research Areas
Cancer
Genetics And Genomics
Health System And Policy