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Should regions of long-range LD in the genome be removed prior to PCA?

April 26, 2017genome LD long-range PCa prior regions removed

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Should regions of long-range LD in the genome be removed prior to PCA?

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Yes, to avoid principal components that are artifacts of long-range LD it is ideal to remove such regions. See Table 1 of Price et al. 2008 AJHG. However, EIGENSTRAT can subsequently be run to compute disease association statistics using the full set of SNPs.