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.

中文翻译：

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百万退伍军人计划中的基因分型阵列设计和数据质量控制。

由退伍军人事务部 (VA) 发起的百万退伍军人计划 (MVP) 旨在征得至少一百万退伍军人的同意后收集生物样本。目前，已从超过 800,000 名注册参与者中收集了血液样本。MVP 队列的规模和多样性，以及广泛的 VA 电子健康记录的可用性，使其成为精准医学的有前途的资源。MVP 正在进行基于阵列的基因分型，以提供整个队列的全基因组扫描，同时进行全基因组测序、甲基化和其他“组学分析”。在这里，我们展示了 MVP 1.0 定制 Axiom 阵列的设计和性能，该阵列被设计和开发为单一检测，可在多种族 MVP 队列中使用。对 485,856 名个体的初始批次开发和进行了统一的遗传质量控制分析，产生了包含 459,777 个独特个体的高质量数据集。668,418个遗传标记通过质量控制，不仅在常见变异上，而且在稀有变异上都显示出高质量的基因型。我们证实，由于非欧洲人占近 30%，MVP 的大量祖先多样性超过了其他大型生物库。我们还通过复制欧洲裔美国人和非裔美国人血统中已建立的与身高的遗传关联来证明 MVP 数据集的质量。该当前数据集已提供给获得批准的 MVP 研究人员，用于全基因组关联研究和其他下游分析。