We used sign tests to compare the overall patterns of results between the Swedish and PGC schizophrenia samples. We used the clumping settings above to derive a filtered set of SNPs. Due to the strong signal and high linkage disequilibrium in the MHC, only one SNP was kept from the extended MHC region. We then determined the number of SNPs whose logistic regression beta coefficient signs were the same between two independent samples. Under the null, the expectation is that 50% of the signs of these SNPs will be the same between two independent sets of results. The significance of the observed proportion was evaluated using the binomial distribution.
