Population structure and relatedness estimates in a Mexican sample

CHIBCHA Consortium

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Population stratification (PS) is a confounding factor in genome-wide association studies (GWASs) and also an interesting process itself. Latin American populations have mixed genetic ancestry, which may account for PS. We have analyzed the relatedness, by means of the identity-by-descent (IBD) estimations, in a sample of 1805 individuals and 1.006.703 autosomal mutations from a case-control study of colorectal cancer in Mexico. When using the recommended protocol for quality control assessment, 402 should have been removed due to relatedness. Our purpose was to analyze this value in the context of an admixed population. For that aim, we reanalyzed the sample using two software designed for admixed populations, obtaining estimates of 110 and 70 related individuals to remove. The results showed that the first estimation of relatedness was an effect of the higher Native American contribution in part of the data samples, being a confounding factor for IBD estimations. We conclude in the importance of considering PS and genetic ancestry in order to avoid spurious results, not only in GWAS but also in relatedness analysis.

Original languageEnglish (US)
Pages (from-to)245-248
Number of pages4
JournalAnnals of Human Genetics
Issue number6
StatePublished - Nov 1 2021


  • admixed populations and population stratification
  • identity-by-descent

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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