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.

中文翻译：

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墨西哥样本中的人口结构和相关性估计

群体分层 (PS) 是全基因组关联研究 (GWAS) 中的一个混杂因素，而且本身也是一个有趣的过程。拉丁美洲人群具有混合遗传血统，这可能是 PS 的原因。我们通过血统同一性 (IBD) 估计分析了来自墨西哥结直肠癌病例对照研究的 1805 个人和 1.006.703 常染色体突变样本中的相关性。当使用推荐的协议进行质量控制评估时，由于相关性，402 应该被删除。我们的目的是在混合人群的背景下分析这个值。为此，我们使用两个专为混合人群设计的软件重新分析了样本，获得了要移除的 110 和 70 名相关个体的估计值。结果表明，相关性的第一个估计是部分数据样本中美洲原住民贡献较高的影响，这是 IBD 估计的混杂因素。我们总结了考虑 PS 和遗传祖先以避免虚假结果的重要性，不仅在 GWAS 中，而且在相关性分析中也是如此。