To complement the GCTA analyses, we also applied ABPA (approximate Bayesian polygenic analysis) 66 to the Sweden + PGC results. Compared to GCTA, ABPA yielded somewhat larger but generally congruent estimates of variance in liability to schizophrenia using HapMap3 data: 0.43 for population risk of 0.01 (95% credible interval 0.38-0.48) and 0.34 for population risk of 0.004 (95% credible interval 0.31-0.37).
