Population substructure and control selection in genome-wide association studies.

In this case, the first two PCs were highly significant, namely a Tracy-Widom test P-value <10 −7 , but the additional lower ranked PCs (third and onwards) had P-value larger than 0.05.

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Population structure in the PLCO prostate cancer study We applied the PCA using the set of 12,898 structure inference SNPs in the original nested case-control study of prostate cancer (PLCOca-PLCOco) and found that the top 4 PCs are strongly significant with P-values less than 10 −4 based on the Tracy Widom test, while the 5 th is borderline significant ( Table 1 ).

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