subjects into three distinct groups. These three groups correspond to the genotypes of a cluster of highly correlated SNPs in 8p23, a region that contains a polymorphic inversion. The same result was found previously in PCA of other European-ancestry populations [Novembre, et al. 2008]. The highly localized features underlying some principal components may limit their usefulness in detecting and controlling for population structure. Moreover, they may even be counterproductive when used as covariates in association testing for traits affected by SNPs in those chromosomal regions. Therefore, when adjusting for potential population structure, we recommend against the use of PCs that are highly correlated with localized SNP clusters.
