values > 0.0001 were used for imputation. Genotypes were imputed to 1000 Genomes using the cosmopolitan reference panel (Phase 3, version 5, NCBI GRCh37; Supplemental Text) using SHAPEIT243 and Minimac344. Imputed SNPs with R2 < 0.30 were excluded, and genotype probabilities were converted to best-guess genotypes if ≥ 0.90. Because some individuals within a family were genotyped on different arrays, families were again evaluated for Mendelian inconsistencies using Pedcheck45, and imputed SNPs were cleaned as described above. All genotyped and imputed SNPs with missing rates <25%, MAF ≥1% and HWE p >1 × 10−6 were included in analyses.
