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Genotyping Array Design and Data Quality Control in the Million Veteran Program.

Publication ,  Journal Article
Hunter-Zinck, H; Shi, Y; Li, M; Gorman, BR; Ji, S-G; Sun, N; Webster, T; Liem, A; Hsieh, P; Devineni, P; Karnam, P; Gong, X; Radhakrishnan, L ...
Published in: Am J Hum Genet
April 2, 2020

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.

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Published In

Am J Hum Genet

DOI

EISSN

1537-6605

Publication Date

April 2, 2020

Volume

106

Issue

4

Start / End Page

535 / 548

Location

United States

Related Subject Headings

  • Whole Genome Sequencing
  • Veterans
  • Quality Control
  • Precision Medicine
  • Polymorphism, Single Nucleotide
  • Middle Aged
  • Male
  • Humans
  • Genotype
  • Genome-Wide Association Study
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Hunter-Zinck, H., Shi, Y., Li, M., Gorman, B. R., Ji, S.-G., Sun, N., … Pyarajan, S. (2020). Genotyping Array Design and Data Quality Control in the Million Veteran Program. Am J Hum Genet, 106(4), 535–548. https://doi.org/10.1016/j.ajhg.2020.03.004
Hunter-Zinck, Haley, Yunling Shi, Man Li, Bryan R. Gorman, Sun-Gou Ji, Ning Sun, Teresa Webster, et al. “Genotyping Array Design and Data Quality Control in the Million Veteran Program.Am J Hum Genet 106, no. 4 (April 2, 2020): 535–48. https://doi.org/10.1016/j.ajhg.2020.03.004.
Hunter-Zinck H, Shi Y, Li M, Gorman BR, Ji S-G, Sun N, et al. Genotyping Array Design and Data Quality Control in the Million Veteran Program. Am J Hum Genet. 2020 Apr 2;106(4):535–48.
Hunter-Zinck, Haley, et al. “Genotyping Array Design and Data Quality Control in the Million Veteran Program.Am J Hum Genet, vol. 106, no. 4, Apr. 2020, pp. 535–48. Pubmed, doi:10.1016/j.ajhg.2020.03.004.
Hunter-Zinck H, Shi Y, Li M, Gorman BR, Ji S-G, Sun N, Webster T, Liem A, Hsieh P, Devineni P, Karnam P, Gong X, Radhakrishnan L, Schmidt J, Assimes TL, Huang J, Pan C, Humphries D, Brophy M, Moser J, Muralidhar S, Huang GD, Przygodzki R, Concato J, Gaziano JM, Gelernter J, O’Donnell CJ, Hauser ER, Zhao H, O’Leary TJ, VA Million Veteran Program, Tsao PS, Pyarajan S. Genotyping Array Design and Data Quality Control in the Million Veteran Program. Am J Hum Genet. 2020 Apr 2;106(4):535–548.
Journal cover image

Published In

Am J Hum Genet

DOI

EISSN

1537-6605

Publication Date

April 2, 2020

Volume

106

Issue

4

Start / End Page

535 / 548

Location

United States

Related Subject Headings

  • Whole Genome Sequencing
  • Veterans
  • Quality Control
  • Precision Medicine
  • Polymorphism, Single Nucleotide
  • Middle Aged
  • Male
  • Humans
  • Genotype
  • Genome-Wide Association Study