A widely used approach to evaluate whether confounding due to population stratification exists is to compute the Genomic Control λ (λGC), defined as the median χ2(1 dof) association statistic across SNPs divided by its theoretical median under the null distribution7–9. A value of λGC≈1 indicates no stratification, whereas λGC>1 indicates stratification or other confounders such as family structure or cryptic relatedness (see below), or differential bias10. P-P plots are a standard tool for visualization of test statistics (Figure 1). Values of λGC<1.05 are generally considered benign, although inflation in λGC is proportional to sample size.
