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Genet Epidemiol. 2019 Feb;43(1):63-81. doi: 10.1002/gepi.22167. Epub 2018 Oct 8.

The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype.

Author information

1
Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington.
2
Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington.
3
Harvard Medical School, Harvard University, Cambridge, Massachusetts.
4
Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
5
Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee.
6
Department of Medicine, Columbia University, New York City, New York.
7
Vanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee.
8
Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
9
Geisinger Research, Rockville, Marland.
10
Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania.
11
Mayo Clinic, Rochester, Minnesota.
12
Program in Medical and Population Genetics, Broad Institute of Massachusetts Technical Institute and Harvard University, Cambridge, Massachusetts.
13
Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, Washington.
14
Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, Maryland.
15
Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
16
National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.

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).

KEYWORDS:

GWAS; electronic medical records; genotypes; herpes zoster; variants

PMID:
30298529
PMCID:
PMC6375696
DOI:
10.1002/gepi.22167
[Indexed for MEDLINE]
Free PMC Article

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