DNA specimens from the CATS sample were genotyped at the Center for Inherited Disease Research (CIDR) using the Illumina Human660W-Quad BeadChip. Genotype and sample QC was as described previously [9]. After initial QC, data were imputed to the 1,000 Genomes Phase 3 European ancestries reference panel using the Michigan Imputation Server. Details on the genotyping QC, and imputation of the COGA samples are described in detail elsewhere [37]. Briefly, samples were genotyped on multiple arrays in multiple labs. A subset of 47,000 common, independent, and high-quality SNPs that were genotyped across all arrays were used to assess duplicate samples, confirm the reported pedigree structure and compute ancestral principal components (PCs). After assignment of individuals in a family to a specific population, family-wise ancestry was designated according to the majority of individual family members. Genotypes were imputed to 1,000 Genomes using the cosmopolitan reference panel (Phase 3, version 5, NCBI GRCh37) using SHAPEIT2 [38] and Minimac3 [39].
