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Genetic ancestry and population structure in the All of Us Research Program cohort

Author

Listed:
  • Shivam Sharma

    (Georgia Institute of Technology
    National Institutes of Health)

  • Shashwat Deepali Nagar

    (Georgia Institute of Technology)

  • Priscilla Pemu

    (Morehouse School of Medicine
    University of Miami)

  • Stephan Zuchner

    (University of Miami
    University of Miami)

  • Leonardo Mariño-Ramírez

    (National Institutes of Health)

  • Robert Meller

    (Morehouse School of Medicine
    University of Miami)

  • I. King Jordan

    (Georgia Institute of Technology)

Abstract

We analyzed participant genomic variant data to characterize population structure and genetic ancestry for the All of Us cohort (n = 297,549). There is substantial population structure in the cohort, with clusters of closely related participants interspersed among less related individuals. Participants show diverse genetic ancestry, with major contributions from European (66.4%), African (19.5%), Asian (7.6%), and American (6.3%) continental ancestry components. Participant genetic similarity clusters show group-specific ancestry, with distinct patterns of continental and subcontinental ancestry among groups. African and American ancestry are enriched in the southeast and southwest regions of the country, respectively, whereas European ancestry is more evenly distributed across the US. The diversity of All of Us participants’ genetic ancestry is negatively correlated with age; younger participants show higher levels of genetic admixture compared to older participants. Our results underscore the ancestral genetic diversity of the All of Us cohort, a crucial prerequisite for genomic health equity.

Suggested Citation

  • Shivam Sharma & Shashwat Deepali Nagar & Priscilla Pemu & Stephan Zuchner & Leonardo Mariño-Ramírez & Robert Meller & I. King Jordan, 2025. "Genetic ancestry and population structure in the All of Us Research Program cohort," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59351-8
    DOI: 10.1038/s41467-025-59351-8
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    References listed on IDEAS

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    1. Noah A Rosenberg & Saurabh Mahajan & Sohini Ramachandran & Chengfeng Zhao & Jonathan K Pritchard & Marcus W Feldman, 2005. "Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure," PLOS Genetics, Public Library of Science, vol. 1(6), pages 1-12, December.
    2. repec:plo:pgen00:1008225 is not listed on IDEAS
    3. Carlos D. Bustamante & Francisco M. De La Vega & Esteban G. Burchard, 2011. "Genomics for the world," Nature, Nature, vol. 475(7355), pages 163-165, July.
    4. Rasmus Nielsen & Joshua M. Akey & Mattias Jakobsson & Jonathan K. Pritchard & Sarah Tishkoff & Eske Willerslev, 2017. "Tracing the peopling of the world through genomics," Nature, Nature, vol. 541(7637), pages 302-310, January.
    5. Eunjung Han & Peter Carbonetto & Ross E. Curtis & Yong Wang & Julie M. Granka & Jake Byrnes & Keith Noto & Amir R. Kermany & Natalie M. Myres & Mathew J. Barber & Kristin A. Rand & Shiya Song & Theodo, 2017. "Clustering of 770,000 genomes reveals post-colonial population structure of North America," Nature Communications, Nature, vol. 8(1), pages 1-12, April.
    6. Alice B. Popejoy & Stephanie M. Fullerton, 2016. "Genomics is failing on diversity," Nature, Nature, vol. 538(7624), pages 161-164, October.
    7. Julian R Homburger & Andrés Moreno-Estrada & Christopher R Gignoux & Dominic Nelson & Elena Sanchez & Patricia Ortiz-Tello & Bernardo A Pons-Estel & Eduardo Acevedo-Vasquez & Pedro Miranda & Carl D La, 2015. "Genomic Insights into the Ancestry and Demographic History of South America," PLOS Genetics, Public Library of Science, vol. 11(12), pages 1-26, December.
    Full references (including those not matched with items on IDEAS)

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