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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.
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BMC Genomic Data

ISSN: 2730-6844

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