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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Related Experiment Video

Updated: Dec 25, 2025

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Genotyping Array Design and Data Quality Control in the Million Veteran Program.

Haley Hunter-Zinck1, Yunling Shi1, Man Li2

  • 1VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA 02130, USA.

American Journal of Human Genetics
|April 4, 2020
PubMed
Summary
This summary is machine-generated.

The Million Veteran Program (MVP) developed a high-quality genetic array for over 450,000 diverse veterans. This resource supports precision medicine research by providing robust genome-wide data for association studies.

Keywords:
GWASMillion Veteran ProgramSNP array designVAbiobankclinical variantsgenetic ancestrygenetic relatednessgenotype dataquality control

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Area of Science:

  • Genomics
  • Biobanking
  • Precision Medicine

Background:

  • The Million Veteran Program (MVP) is a large-scale initiative by the Department of Veterans Affairs (VA) collecting biosamples and health records from veterans.
  • MVP aims to enroll at least one million veterans, with over 800,000 already participating, creating a valuable cohort for research.

Purpose of the Study:

  • To present the design and performance of the MVP 1.0 custom Axiom array, a genome-wide genotyping assay for the multi-ethnic MVP cohort.
  • To establish a high-quality genetic dataset from the MVP cohort for precision medicine and genome-wide association studies.

Main Methods:

  • Design and development of the MVP 1.0 custom Axiom array for a multi-ethnic cohort.
  • Implementation of a unified genetic quality-control analysis on an initial cohort of 485,856 individuals.
  • Array-based genotyping and quality control yielding a dataset of 459,777 unique individuals with 668,418 genetic markers.

Main Results:

  • A high-quality dataset of 459,777 individuals with 668,418 genetic markers passing quality control.
  • Demonstrated high-quality genotypes for both common and rare variants.
  • Confirmed substantial ancestral diversity in the MVP cohort, with nearly 30% non-European individuals, surpassing other large biobanks.
  • Replicated established genetic associations with height in European Americans and African Americans, validating the dataset's quality.

Conclusions:

  • The MVP 1.0 Axiom array and resulting dataset provide a high-quality resource for genetic research in a diverse veteran population.
  • The MVP cohort's size, diversity, and linked electronic health records offer significant potential for advancing precision medicine.
  • The dataset is available to approved researchers, with future data releases planned as the cohort expands.