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Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort.


ABSTRACT: The Kaiser Permanente (KP) Research Program on Genes, Environment and Health (RPGEH), in collaboration with the University of California-San Francisco, undertook genome-wide genotyping of >100,000 subjects that constitute the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. The project, which generated >70 billion genotypes, represents the first large-scale use of the Affymetrix Axiom Genotyping Solution. Because genotyping took place over a short 14-month period, creating a near-real-time analysis pipeline for experimental assay quality control and final optimized analyses was critical. Because of the multi-ethnic nature of the cohort, four different ethnic-specific arrays were employed to enhance genome-wide coverage. All assays were performed on DNA extracted from saliva samples. To improve sample call rates and significantly increase genotype concordance, we partitioned the cohort into disjoint packages of plates with similar assay contexts. Using strict QC criteria, the overall genotyping success rate was 103,067 of 109,837 samples assayed (93.8%), with a range of 92.1-95.4% for the four different arrays. Similarly, the SNP genotyping success rate ranged from 98.1 to 99.4% across the four arrays, the variation depending mostly on how many SNPs were included as single copy vs. double copy on a particular array. The high quality and large scale of genotype data created on this cohort, in conjunction with comprehensive longitudinal data from the KP electronic health records of participants, will enable a broad range of highly powered genome-wide association studies on a diversity of traits and conditions.

SUBMITTER: Kvale MN 

PROVIDER: S-EPMC4574249 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort.

Kvale Mark N MN   Hesselson Stephanie S   Hoffmann Thomas J TJ   Cao Yang Y   Chan David D   Connell Sheryl S   Croen Lisa A LA   Dispensa Brad P BP   Eshragh Jasmin J   Finn Andrea A   Gollub Jeremy J   Iribarren Carlos C   Jorgenson Eric E   Kushi Lawrence H LH   Lao Richard R   Lu Yontao Y   Ludwig Dana D   Mathauda Gurpreet K GK   McGuire William B WB   Mei Gangwu G   Miles Sunita S   Mittman Michael M   Patil Mohini M   Quesenberry Charles P CP   Ranatunga Dilrini D   Rowell Sarah S   Sadler Marianne M   Sakoda Lori C LC   Shapero Michael M   Shen Ling L   Shenoy Tanu T   Smethurst David D   Somkin Carol P CP   Van Den Eeden Stephen K SK   Walter Lawrence L   Wan Eunice E   Webster Teresa T   Whitmer Rachel A RA   Wong Simon S   Zau Chia C   Zhan Yiping Y   Schaefer Catherine C   Kwok Pui-Yan PY   Risch Neil N  

Genetics 20150619 4


The Kaiser Permanente (KP) Research Program on Genes, Environment and Health (RPGEH), in collaboration with the University of California-San Francisco, undertook genome-wide genotyping of >100,000 subjects that constitute the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. The project, which generated >70 billion genotypes, represents the first large-scale use of the Affymetrix Axiom Genotyping Solution. Because genotyping took place over a short 14-month period, creating  ...[more]

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