per locus and study site. Our analyses showed that DNA from a few population samples showed excess missingness for two SNPs, rs4742408 and rs7869239, relative to the remaining population samples. Specifically three population samples showed more than 7% missing genotypes for rs4742408 and rs7869239 whereas the remaining population samples had about 1% or less missing genotypes. Therefore, for these loci we deleted genotypes only from the samples showing excess missingness. As a final quality control step, we then evaluated missing genotypes for the remaining loci. If more than five loci were missing genotypes, the individual’s data was removed from analysis. By this criterion 76 additional families became uninformative for family-based association analysis, leaving 1,443 families for association analysis. The Finnish autism samples were genotyped in the Peltonen lab, and the Iranian trios were genotyped at the Broad Institute using very similar protocols. All samples were genotyped using aliquots from the same pooled primers and probes.
