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

The eMERGE Network

Research output: Contribution to journalArticle

3 Citations (Scopus)

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).

Original languageEnglish (US)
JournalGenetic Epidemiology
DOIs
StateAccepted/In press - Jan 1 2018

Fingerprint

Electronic Health Records
Herpes Zoster
Genomics
Medical Records
Genotype
Genome
Phenotype
Chromosomes, Human, Pair 6
Chromosomes, Human, Pair 3
HLA-B Antigens
Epigenomics
Quality Control
Haplotypes
Nucleotides
Binding Sites
Medicine
Research

Keywords

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

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)

Cite this

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title = "The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype",
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 = "electronic medical records, genotypes, GWAS, herpes zoster, variants",
author = "{The eMERGE Network} and Stanaway, {Ian B.} and Hall, {Taryn O.} and Rosenthal, {Elisabeth A.} and Melody Palmer and Vivek Naranbhai and Rachel Knevel and Bahram Namjou-Khales and Carroll, {Robert J.} and Krzysztof Kiryluk and Gordon, {Adam S.} and Jodell Linder and Howell, {Kayla Marie} and Mapes, {Brandy M.} and Lin, {Frederick T.J.} and Joo, {Yoonjung Yoonie} and Hayes, {M. Geoffrey} and Gharavi, {Ali G.} and Pendergrass, {Sarah A.} and Ritchie, {Marylyn D.} and {De Andrade}, Mariza and Croteau-Chonka, {Damien C.} and Soumya Raychaudhuri and Weiss, {Scott T.} and Matt Lebo and Amr, {Sami S.} and David Carrell and Larson, {Eric B.} and Chute, {Christopher G.} and Rasmussen-Torvik, {Laura Jarmila} and Roy-Puckelwartz, {Megan J.} and Patrick Sleiman and Hakon Hakonarson and Rongling Li and Karlson, {Elizabeth W.} and Peterson, {Josh F.} and Kullo, {Iftikhar Jan} and Rex Chisholm and Denny, {Joshua Charles} and Jarvik, {Gail P.} and Crosslin, {David R.}",
year = "2018",
month = "1",
day = "1",
doi = "10.1002/gepi.22167",
language = "English (US)",
journal = "Genetic Epidemiology",
issn = "0741-0395",
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T1 - The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype

AU - The eMERGE Network

AU - Stanaway, Ian B.

AU - Hall, Taryn O.

AU - Rosenthal, Elisabeth A.

AU - Palmer, Melody

AU - Naranbhai, Vivek

AU - Knevel, Rachel

AU - Namjou-Khales, Bahram

AU - Carroll, Robert J.

AU - Kiryluk, Krzysztof

AU - Gordon, Adam S.

AU - Linder, Jodell

AU - Howell, Kayla Marie

AU - Mapes, Brandy M.

AU - Lin, Frederick T.J.

AU - Joo, Yoonjung Yoonie

AU - Hayes, M. Geoffrey

AU - Gharavi, Ali G.

AU - Pendergrass, Sarah A.

AU - Ritchie, Marylyn D.

AU - De Andrade, Mariza

AU - Croteau-Chonka, Damien C.

AU - Raychaudhuri, Soumya

AU - Weiss, Scott T.

AU - Lebo, Matt

AU - Amr, Sami S.

AU - Carrell, David

AU - Larson, Eric B.

AU - Chute, Christopher G.

AU - Rasmussen-Torvik, Laura Jarmila

AU - Roy-Puckelwartz, Megan J.

AU - Sleiman, Patrick

AU - Hakonarson, Hakon

AU - Li, Rongling

AU - Karlson, Elizabeth W.

AU - Peterson, Josh F.

AU - Kullo, Iftikhar Jan

AU - Chisholm, Rex

AU - Denny, Joshua Charles

AU - Jarvik, Gail P.

AU - Crosslin, David R.

PY - 2018/1/1

Y1 - 2018/1/1

N2 - 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).

AB - 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).

KW - electronic medical records

KW - genotypes

KW - GWAS

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KW - variants

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U2 - 10.1002/gepi.22167

DO - 10.1002/gepi.22167

M3 - Article

JO - Genetic Epidemiology

JF - Genetic Epidemiology

SN - 0741-0395

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