Using GCTA version 1.04(42) we computed a genetic relatedness matrix for each of the two SNP sets, rare and common. Because the sample is composed of families, and familial relationships include non-additive and shared environmental effects, we restricted the GCTA method only to nominally unrelated individuals by using individuals with a genetic relatedness less than .025 based on common SNPs, a threshold that is standard practice in these analyses. The genetic relatedness estimate used is a distance metric analogous to the average SNP correlation between two individuals. To test the effect of this cutoff, we evaluated selected results at many cutoffs ranging from .01 to 1.0 (Figure S12 in Supplement 1).
