Genotyping Array Design and Data Quality Control in the Million Veteran Program
The Million Veteran Program (MVP), initiated by the Department of Veterans Affairs (VA), aims to collect biosamples with consent 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...
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| Veröffentlicht in: | American journal of human genetics 2020-04, Vol.106 (4), p.535-548 |
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| creator | Hunter-Zinck, Haley Shi, Yunling Li, Man Gorman, Bryan R. Ji, Sun-Gou Sun, Ning Webster, Teresa Liem, Andrew Hsieh, Paul Devineni, Poornima Karnam, Purushotham Gong, Xin Radhakrishnan, Lakshmi Schmidt, Jeanette Assimes, Themistocles L. Huang, Jie Pan, Cuiping Humphries, Donald Brophy, Mary Moser, Jennifer Muralidhar, Sumitra Huang, Grant D. Przygodzki, Ronald Concato, John Gaziano, John M. Gelernter, Joel O’Donnell, Christopher J. Hauser, Elizabeth R. Zhao, Hongyu O’Leary, Timothy J. Tsao, Philip S. Pyarajan, Saiju |
| description | The Million Veteran Program (MVP), initiated by the Department of Veterans Affairs (VA), aims to collect biosamples with consent 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 a 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 the 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 that, with non-European individuals making up nearly 30%, MVP’s substantial ancestral diversity surpasses that of 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 dataset 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. |
| doi_str_mv | 10.1016/j.ajhg.2020.03.004 |
| format | Article |
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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 a 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 the 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 that, with non-European individuals making up nearly 30%, MVP’s substantial ancestral diversity surpasses that of 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 dataset has been made available to approved MVP researchers for genome-wide association studies and other downstream analyses. 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We confirmed that, with non-European individuals making up nearly 30%, MVP’s substantial ancestral diversity surpasses that of 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 dataset has been made available to approved MVP researchers for genome-wide association studies and other downstream analyses. 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We confirmed that, with non-European individuals making up nearly 30%, MVP’s substantial ancestral diversity surpasses that of 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 dataset 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.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>32243820</pmid><doi>10.1016/j.ajhg.2020.03.004</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | American journal of human genetics, 2020-04, Vol.106 (4), p.535-548 |
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| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals Complete; Cell Press Free Archives; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Aged Aged, 80 and over biobank clinical variants Cohort Studies Ethnic Groups - genetics Female genetic ancestry Genetic Markers - genetics genetic relatedness Genome-Wide Association Study - methods Genotype genotype data GWAS Humans Male Middle Aged Million Veteran Program Polymorphism, Single Nucleotide - genetics Precision Medicine - methods Quality Control SNP array design Veterans Whole Genome Sequencing - methods |
| title | Genotyping Array Design and Data Quality Control in the Million Veteran Program |
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