showed that SNPs with MAF<0.05 accounted for 30% of the total TS heritability and 0% of the total OCD heritability. To ensure that the difference between TS and OCD rare SNP heritability estimates were not due to subtle population substructure in the TS sample, we conducted an additional analysis which further partitioned the MAF<5% bin by chromosome. We then compared the estimate of heritability calculated by summing each chromosome (h2 = 12.3, se = 0.08) to the estimate of heritability based on all MAF<5% SNPs in a single analysis (h2 = 12.7, se = 0.04) and found no significant difference. If population substructure was present in the TS sample and was a source of bias contributing to the increased heritability identified in the rare bin, we would have expected to see inflation of the heritability estimate due to LD between chromosomes when partitioned by chromosome and then summed [51]. We can therefore reject the hypothesis that the rare variant heritability in TS is due to population substructure.
