We observed a large genome-wide ‘inflation’ factor of the test statistic for association even after we corrected each study’s test statistics by its individual inflation factor (single λGC = 1.94). At least two phenomena could have contributed to this observation. First, as described previously10, highly polygenic models of inheritance are expected to increase the genomic inflation factor to levels comparable to what we observe. Second, height is particularly susceptible to confounding by population ancestry (stratification), which can also lead to inflation of the test statistics. We addressed these possibilities by comparing our results with those obtained using more stringent corrections for stratification (linear mixed models), and with results obtained in subsets of studies in which a purely family-based analysis was feasible, and by performing a within-family prediction analysis which partitioned the variance in the genetic predictor into the contributions of true associations and population stratification.
