the 1000 Genomes Phase 316 cosmopolitan reference panel), and derive ancestry-specific principal components for inclusion in analyses (appendix p 10). Sample and variant quality-controlled procedures, including filters for call rate, heterozygosity, and departure from Hardy-Weinberg equilibrium, were done within each ancestry group in each sample. Each group was phased using SHAPEIT17 and imputed using IMPUTE218 to the 1000 Genomes Phase 316 cosmopolitan reference panel (appendix pp 10–11). Duplicate individuals were removed and individuals who were cryptically related across groups were excluded from all but one group (appendix p 12). Single-nucleotide polymorphisms (SNPs) were filtered for INFO score of more than 0·8 and minor allele frequency of at least 0·01 before meta-analysis (appendix pp 13–14).
