are preferentially biased against heterozygotes or rare homozygotes, significant, artificial over-transmission of the common allele is expected 28,29. To achieve comparable quality for the NIMH dataset, we filtered on 96% completeness and fewer than 4 MEs. Our final QQ plot for the combined dataset is shown in Supplementary Figure 1 and has a λ ~ 1.03, less than that observed in the Wellcome Trust Case Control Consortium paper for five of the seven phenotypes studied 30. The combined data set, consisting of 1,031 families (856 with two parents) and a total of 1,553 affected offspring, was employed for association testing.
