Journal article
Genotyping, sequencing and analysis of 140,000 adults from Mexico City
- Abstract:
- The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Version of record, pdf, 19.5MB, Terms of use)
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- Publisher copy:
- 10.1038/s41586-023-06595-3
Authors
Contributors
+ Regeneron Genetics Center
- Role:
- Contributor
+ Mexico City Prospective Study
- Role:
- Contributor
- Publisher:
- Springer Nature
- Journal:
- Nature More from this journal
- Volume:
- 622
- Issue:
- 7984
- Pages:
- 784-793
- Place of publication:
- England
- Publication date:
- 2023-10-11
- Acceptance date:
- 2023-08-31
- DOI:
- EISSN:
-
1476-4687
- ISSN:
-
0028-0836
- Pmid:
-
37821707
- Language:
-
English
- Keywords:
- Pubs id:
-
1544803
- Local pid:
-
pubs:1544803
- Deposit date:
-
2023-12-04
Terms of use
- Copyright holder:
- Ziyatdinov et al.
- Copyright date:
- 2023
- Rights statement:
- © 2023, The Author(s). Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
- Notes:
- This research was funded in whole or in part by the Wellcome Trust (203141/Z/16/Z). For the purposes of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission.
- Licence:
- CC Attribution (CC BY)
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