Axiom panafr snp array

Genotyping was performed using either the Affymetrix Axiom PANAFR SNP array or the Illumina Multi-Ethnic Global Array (MEGA) as previously described^{22 (link)}. Quality control was performed for each of the arrays separately, resulting in a sample-level genotype call rate of at least 0.95 for all samples. Imputation was performed using the African Genome Resources Haplotype Reference Panel via the Sanger Imputation Service.

Genotyping for the AADM study was performed using either the Affymetrix Axiom PANAFR SNP array or the Illumina’s Multi-Ethnic Global Array (MEGA) [31 (link)]. Quality control was performed for each of the arrays separately, resulting in a sample level genotype call rate of at least 0.95 for all samples. For the replication cohorts, genotyping was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 [39 (link)]. For all cohorts, the SNP datasets were filtered for missingness per marker (> 0.05), minor allele frequency (< 0.01), and Hardy-Weinberg equilibrium (P value ≤ 1 × 10⁻⁶). Imputation for all cohorts was performed using the African Genome Resources Haplotype Reference Panel via the Sanger imputation Service [40 ]. Quality of imputation was evaluated using INFO scores and only SNPs with INFO scores > 0.3 were retained. After filtering, 18,199,418 variants remained in the final dataset for AADM and 18,093,757 variants for replication cohorts. We checked for population stratification using the “epacts-pca-plot” function in the EPACTS software package (version 3.2.6) [41 ] and identified three significant principal components (PCs) for AADM, one for HUFS, and two for the other replication cohorts [42 ].