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Mexico City Prospective Study

Summary

The Mexico City Prospective Study (MCPS) is a prospective cohort of over 150,000 adults recruited from the Coyoacán and Iztapalapa districts of Mexico City between 1998 and 2004 [1]. It has generated extensive genomic data and is notable for extensive embedded family networks, making it a key test case for genetic-association methods that must jointly handle admixture and relatedness [1].

Cohort Characteristics

  • Recruitment: over 150,000 adults recruited 1998–2004 from the Coyoacán and Iztapalapa districts of Mexico City.[1]
  • Relatedness: extensive embedded family networks — reported elsewhere in the same source as 70% (Introduction) and 71% (Results) of participants having at least one third-degree-or-closer relative within the study — making standard relatedness-naive GWAS pipelines poorly suited to this cohort.[1]

Provenance note: the two figures above are drawn from [1] (Tan et al., full text inspected), which in turn attributes the recruitment description and relatedness statistic to the cohort-profile paper by Tapia-Conyer et al. (2006)[2] and the genomic-characterization paper by Ziyatdinov et al. (2023)[3], respectively. Those two primary sources have been bibliographically identified (titles/DOIs confirmed) but not independently read in full — see them directly for the original figures and any refinements from peer review.

Use in Tractor-Mix Validation

Tractor-Mix was applied to body mass index (BMI) in 33,500 MCPS participants restricted to <2.5% East Asian/African global ancestry and modeled as 2-way Indigenous American (IAM, mean 85.1%) / European (EUR, mean 14.9%) admixture.[1] Genomic-control inflation was 1.40 for unadjusted PLINK regression versus 1.24–1.27 for relatedness-aware methods (GMMAT, Tractor-Mix). The known FTO BMI locus was significant only in the EUR-specific analysis, while other genome-wide-significant hits were IAM-specific, including a joint-test-only association near the ZNF646P1 pseudogene (rs9568859). See Tractor-Mix for full results.

Citations

[1] Tan, T. et al. (2025). Extending Genome-Wide Association Studies to admixed cohorts with high degrees of relatedness. medRxiv preprint. DOI: 10.1101/2025.05.27.25328444. Source: 2025.05.27.25328444v1.full.md. Supports: recruitment description, relatedness statistics, and the Tractor-Mix BMI validation analysis described above.

[2] Tapia-Conyer, R. et al. (2006). Cohort profile: the Mexico City Prospective Study. International Journal of Epidemiology, 35(2), 243–249. DOI: 10.1093/ije/dyl042. Not independently inspected — bibliographic identification only (cited by [1] as the source of the recruitment/relatedness description).

[3] Ziyatdinov, A. et al. (2023). Genotyping, sequencing and analysis of 140,000 adults from Mexico City. Nature, 622, 784–793. DOI: 10.1038/s41586-023-06595-3. Not independently inspected — bibliographic identification only (cited by [1] as the source of the relatedness statistic).