Premium
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(s) -
Stanaway Ian B.,
Hall Taryn O.,
Rosenthal Elisabeth A.,
Palmer Melody,
Naranbhai Vivek,
Knevel Rachel,
NamjouKhales Bahram,
Carroll Robert J.,
Kiryluk Krzysztof,
Gordon Adam S.,
Linder Jodell,
Howell Kayla Marie,
Mapes Brandy M.,
Lin Frederick T.J.,
Joo Yoonjung Yoonie,
Hayes M. Geoffrey,
Gharavi Ali G.,
Pendergrass Sarah A.,
Ritchie Marylyn D.,
Andrade Mariza,
CroteauChonka Damien C.,
Raychaudhuri Soumya,
Weiss Scott T.,
Lebo Matt,
Amr Sami S.,
Carrell David,
Larson Eric B.,
Chute Christopher G.,
RasmussenTorvik Laura Jarmila,
RoyPuckelwartz Megan J.,
Sleiman Patrick,
Hakonarson Hakon,
Li Rongling,
Karlson Elizabeth W.,
Peterson Josh F.,
Kullo Iftikhar J.,
Chisholm Rex,
Denny Joshua Charles,
Jarvik Gail P.,
Crosslin David R.
Publication year - 2019
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.22167
Subject(s) - imputation (statistics) , genome wide association study , genotype , genomics , genetics , single nucleotide polymorphism , biology , genetic association , computational biology , missing data , computer science , genome , gene , machine learning
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).