Measuring genetic variation in the multi-ethnic Million Veteran Program (MVP)
Measuring genetic variation in the multi-ethnic Million Veteran Program (MVP)
Abstract The Million Veteran Program (MVP), initiated by the Department of Veterans Affairs (VA), aims to collect consented biosamples from at least one million Veterans. Presently, blood samples have been collected from over 800,000 enrolled participants. The size and diversity of the MVP cohort, as well as the availability of extensive VA electronic health records make it a promising resource for precision medicine. MVP is conducting array-based genotyping to provide genome-wide scan of the entire cohort, in parallel with whole genome sequencing, methylation, and other omics assays. Here, we present the design and performance of MVP 1.0 custom Axiom? array, which was designed and developed as a single assay to be used across the multi-ethnic MVP cohort. A unified genetic quality control analysis was developed and conducted on an initial tranche of 485,856 individuals leading to a high-quality dataset of 459,777 unique individuals. 668,418 genetic markers passed quality control and showed high quality genotypes not only on common variants but also on rare variants. We confirmed the substantial ancestral diversity of MVP with nearly 30% non-European individuals, surpassing other large biobanks. We also demonstrated the quality of the MVP dataset by replicating established genetic associations with height in European Americans and African Americans ancestries. This current data set has been made available to approved MVP researchers for genome-wide association studies and other downstream analyses. Further data releases will be available for analysis as recruitment at the VA continues and the cohort expands both in size and diversity.
Hauser Elizabeth R.、Tsao Philip S.、Humphries Donald、Brophy Mary、Moser Jennifer、Przygodzki Ronald、Liem Andrew、Hsieh Paul、Karnam Purushotham、Radhakrishnan Lakshmi、Schmidt Jeanette、Assimes Themistocles L.、Zhao Hongyu、O?ˉDonnell Christopher J.、Pyarajan Saiju、Huang Grant D.、Concato John、Gorman Bryan R.、Webster Teresa、O?ˉLeary Timothy J.、Sun Ning、Shi Yunling、Pan Cuiping、Ji Sun-Gou、Huang Jie、Hunter-Zinck Haley、Li Man、Gelernter Joel、Devineni Poornima、Muralidhar Sumitra、on behalf of the VA Million Veteran Program、Gaziano John M.
Durham VA Health System||Department of Medicine, Duke UniversityVA Palo Alto Health Care System||Department of Medicine, Stanford University School of MedicineVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemOffice of Research and Development (ORD), Veterans Health AdministrationOffice of Research and Development (ORD), Veterans Health AdministrationVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare System||Booz Allen Hamilton Inc.VA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemThermo Fisher ScientificThermo Fisher ScientificVA Palo Alto Health Care System||Department of Medicine, Stanford University School of MedicineVA Connecticut Healthcare System, VA Cooperative Studies Program||Yale University School of MedicineVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare System||Department of Medicine, Brigham and Women?ˉs Hospital and Harvard School of MedicineOffice of Research and Development (ORD), Veterans Health AdministrationVA Connecticut Healthcare System, VA Cooperative Studies Program||Yale University School of MedicineVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare System||Booz Allen Hamilton Inc.Thermo Fisher ScientificOffice of Research and Development (ORD), Veterans Health AdministrationVA Connecticut Healthcare System, VA Cooperative Studies Program||Yale University School of MedicineVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemVA Palo Alto Health Care System||Department of Medicine, Stanford University School of MedicineVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare System||Seven Bridges Inc.VA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare System||Department of Internal Medicine, University of Utah School of MedicineVA Connecticut Healthcare System, VA Cooperative Studies Program||Yale University School of MedicineVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare SystemOffice of Research and Development (ORD), Veterans Health AdministrationVA Boston Healthcare System, VA Cooperative Studies Program, VA Boston Healthcare System||Department of Medicine, Brigham and Women?ˉs Hospital and Harvard School of Medicine
遗传学生物科学研究方法、生物科学研究技术生物科学现状、生物科学发展
VAMillion Veteran Programgenotype dataquality controlgenetic ancestrygenetic relatedness
Hauser Elizabeth R.,Tsao Philip S.,Humphries Donald,Brophy Mary,Moser Jennifer,Przygodzki Ronald,Liem Andrew,Hsieh Paul,Karnam Purushotham,Radhakrishnan Lakshmi,Schmidt Jeanette,Assimes Themistocles L.,Zhao Hongyu,O?ˉDonnell Christopher J.,Pyarajan Saiju,Huang Grant D.,Concato John,Gorman Bryan R.,Webster Teresa,O?ˉLeary Timothy J.,Sun Ning,Shi Yunling,Pan Cuiping,Ji Sun-Gou,Huang Jie,Hunter-Zinck Haley,Li Man,Gelernter Joel,Devineni Poornima,Muralidhar Sumitra,on behalf of the VA Million Veteran Program,Gaziano John M..Measuring genetic variation in the multi-ethnic Million Veteran Program (MVP)[EB/OL].(2025-03-28)[2025-05-01].https://www.biorxiv.org/content/10.1101/2020.01.06.896613.点此复制
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