MVP Genotyping and Imputation Protocol

We genotyped 468,961 participants who enrolled in MVP between 2011 and 2017 with a customized Affymetrix Axiom array in two batches. The first batch including 359,964 participants and the second batch including 108,997 participants. The genotyping data generated underwent extensive quality control (QC)^{58 (link)}. We initially imputed to the 1000 Genomes phase 3 version 5 reference panel (1000G)^{59 (link)} in each batch of genotyped data separately using EAGLE v2.3^{60 (link)} and Minimac3^{61 (link)} before joint imputation was performed in the two batches combined using EAGLE v2.4 and Minimac4. Prior to imputation, variants that were poorly called (genotype missingness > 5%) or that deviated from their expected allele frequency observed in the reference data (1000G) were excluded. Genotyped SNPs were interpolated into the imputation file.

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Tcheandjieu C., Zhu X., Hilliard A.T., Clarke S.L., Napolioni V., Ma S., Lee K.M., Fang H., Chen F., Lu Y., Tsao N.L., Raghavan S., Koyama S., Gorman B.R., Vujkovic M., Klarin D., Levin M.G., Sinnott-Armstrong N., Wojcik G.L., Plomondon M.E., Maddox T.M., Waldo S.W., Bick A.G., Pyarajan S., Huang J., Song R., Ho Y.L., Buyske S., Kooperberg C., Haessler J., Loos R.J., Do R., Verbanck M., Chaudhary K., North K.E., Avery C.L., Graff M., Haiman C.A., Le Marchand L., Wilkens L.R., Bis J.C., Leonard H., Shen B., Lange L.A., Giri A., Dikilitas O., Kullo I.J., Stanaway I.B., Jarvik G.P., Gordon A.S., Hebbring S., Namjou B., Kaufman K.M., Ito K., Ishigaki K., Kamatani Y., Verma S.S., Ritchie M.D., Kember R.L., Baras A., Lotta L.A., Japan B., Kathiresan S., Hauser E.R., Miller D.R., Lee J.S., Saleheen D., Reaven P.D., Cho K., Gaziano J.M., Natarajan P., Huffman J.E., Voight B.F., Rader D.J., Chang K.M., Lynch J.A., Damrauer S.M., Wilson P.W., Tang H., Sun Y.V., Tsao P.S., O’Donnell C.J, & Assimes T.L. (2022). Large-scale genome-wide association study of coronary artery disease in genetically diverse populations. Nature medicine, 28(8), 1679-1692.

Publication 2022

Axiom array

Eagle Genomes Joint Snps

Corresponding Organization : VA Palo Alto Health Care System

Other organizations : Università di Camerino, Stanford University, VA Salt Lake City Healthcare System, University of Southern California, Vanderbilt University Medical Center, University of Pennsylvania, VA Eastern Colorado Health Care System, RIKEN Center for Integrative Medical Sciences, VA Boston Healthcare System, Philadelphia VA Medical Center, Johns Hopkins University, BJC HealthCare, Rutgers, The State University of New Jersey, Fred Hutch Cancer Center, Icahn School of Medicine at Mount Sinai, University of North Carolina at Chapel Hill, Cancer Center of Hawaii, University of Hawaiʻi at Mānoa, University of Hawaii System, University of Washington, National Institute on Aging, National Institutes of Health, The Medical Center of Aurora, Mayo Clinic in Arizona, University of Washington Medical Center, Northwestern University, Marshfield Clinic, Cincinnati Children's Hospital Medical Center, Regeneron (United States), Broad Institute, Durham VA Health Care System, VA New England Healthcare System, Phoenix VA Health Care System, Brigham and Women's Hospital, Harvard University, Atlanta Medical Center, Atlanta VA Medical Center, Atlanta VA Health Care System, Cardiovascular Institute of the South

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Variable analysis

independent variables

Genotyping in two batches (batch 1 with 359,964 participants and batch 2 with 108,997 participants)

dependent variables

Genotyping data

control variables

Extensive quality control (QC) of the genotyping data
Imputation to the 1000 Genomes phase 3 version 5 reference panel
Imputation using EAGLE v2.3 and Minimac3 for each batch separately
Joint imputation of the two batches using EAGLE v2.4 and Minimac4
Exclusion of variants that were poorly called (genotype missingness > 5%) or deviated from their expected allele frequency observed in the reference data (1000G)
Interpolation of genotyped SNPs into the imputation file

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