UKB provides genotypes obtained from two closely related genotyping arrays: the UK BiLEVE Axiom Array and the UKB Axiom Array, with additional variants imputed using the Haplotype Reference Consortium and the UK10K + 1000 Genomes reference panels. Full genotyping and quality control details are described by Bycroft et al. and are publicly available. 23 Using the phased haplotype data supplied by UKB, we derived the two APOE alleles for each participant, based on single nucleotide polymorphism (SNP) markers rs429358 and rs7412 on chromosome 19. The APOE genotype of each participant was then assigned based on the combination of the two alleles. The resulting APOE allele and genotype frequencies before and after sample filtering are shown in Tables S3 and S4 in supporting information.
