Pharmacogenomic variation in the Malagasy population: implications for the antimalarial drug primaquine metabolism

In the present study, the authors performed genome-wide SNP typing of 55 Malagasy samples with the Infinium Multi-Ethnic Genotyping Array (MEGA) and analyzed data with a focus on a set of 28 pharmacogenes (Supplementary Table 1).

QC steps were followed as recommended by Illumina [42,45] and have been described by various authors [46,47] (Supplementary Document 1).

The MAF distribution of the polymorphic SNPs in four classes (rare, <1%; low, 1–5%; moderate, >5–10%; and high, >10%) is presented in Supplementary Table 2

For the polymorphic SNPs, their locations, SNP IDs, genomic sequence positions and variant impacts, the star alleles/suballeles they represent and their MAFs, are presented in Supplementary Table 3 in chromosomal order.

The majority of these SNPs are intronic (n = 384), whereas 110 are in coding regions or impact splicing; the latter are presented separately in Supplementary Table 4.

Their distribution, CNV confidence scores and sizes are presented in Supplementary Table 5.

The same CNVs were identified in more than one Malagasy sample; examples and selected results are presented in Supplementary Table 6