The software package PLINK v1.07 (Purcell et al. 2007) was used to calculate pairwise identity-by-descent (IBD) estimates of 100 000 SNPs, which were not in linkage disequilibrium with each other, to verify the reported pedigree structure of the 118 families. Based on these IBDs, some family structures were modified. Using the software PEDCHECK v1.1 (O'Connell & Weeks 1998) on the modified pedigrees, 2899 SNPs with 2 or more inconsistencies with Mendelian inheritance were identified and removed. Ethnic stratification was assessed with EIGENSTRAT (Price et al. 2006) using the 100 000 SNPs and the HapMap Caucasian reference samples, and no individual was excluded based on the EIGENSTRAT v3.0 results.
