DNA for genotyping was obtained from the cerebella of samples in the collection and performed with either the Illumina Human Hap 650v3,1M Duo V3, or Omni 5M BeadArrays as previously described1. We had genotype data on 520/526 samples measured on the Illumina 450k. Genotypes were called separately by genotyping platform using the crlmm software59, and then cleaned separately for imputation (retaining SNPs with MAF > 0.5% and genotyping missing rate < 10%, then checking sex and heterozygosity)60. Genotypes were phased into haplotypes using SHAPEIT261 and imputed in 6MB chunks using Impute262 to the 1000 Genomes Phase 3 variant set for the autosomes and then Phase 1 variant set for chrX (as Phase 3 data is not available yet). Imputed genotypes were merged across the three platforms following imputation, and SNPs with MAF > 5%, HWE p-value > 1×10−6, and missing rate < 10% were retained across the 520 samples. LD-pruning generated an independent set of SNPs to perform genome-wide clustering to obtain multidimensional scaling (MDS) components for quantitative measures of ancestry.
