Chunk #20 — Material and Methods — Impact on Power of Ancestrally Poorly-Matched Public Controls and Batch Genotype Effects

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Using public control genotype data to increase power and decrease cost of case-control genetic association studies.

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controls, we calculated power after correcting for the systematic batch effects across all SNPs by multiplying the critical value of the 1 df chi-square distribution corresponding to p = 1.0×10−7 (i.e. 28.373) by the mean test statistic value, μ (Reich and Goldstein, 2001). For each two-stage study, the stage 1 test-statistic critical value was multiplied by the corresponding mean test statistic value, μ, determined by the stage 1 sample composition.