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Table 2 False Positive Rate of Matched and PC adjusted Unmatched GWAS

From: Clustering by genetic ancestry using genome-wide SNP data

Scenario Cases/Controls False Positive Rate*
Matched 2000/2000 5.00E-07
Unmatched + PCs 2000/2000 8.00E-07
Unmatched + PCs 2000/2250 9.00E-07
Unmatched + PCs 2000/2500 1.30E-06
Unmatched + PCs 2000/2750 1.20E-06
Unmatched + PCs 2000/3000 9.00E-07
Unmatched + PCs 2000/3250 1.00E-06
Unmatched + PCs 2000/3500 8.00E-07
Unmatched + PCs 2000/3750 9.00E-07
Unmatched + PCs 2000/4000 8.00E-07
  1. *False positive rate with a p-value cut-off of 1E-06
  2. We report the false positive rate of a matched GWAS and compare it to PC-adjusted unmatched GWASs with varying number of controls. The false positive rate is computed using a p-value cut-off of 1E-06.