Extended Data Fig. 2: Schematic illustration of method used to construct scaffold variants within multi-ancestry HLA reference panel. | Nature Protocols

Extended Data Fig. 2: Schematic illustration of method used to construct scaffold variants within multi-ancestry HLA reference panel.

From: Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

Extended Data Fig. 2

We extracted SNP variants within MHC region in 1000 Genomes Project (1KG) samples. We only retained variants that were included in major genotyping arrays (Illumina Multi-Ethnic Genotyping Array, Global Screening Array, OmniExpressExome, and Human Core Exome), colored in teal. We then quality controlled each of the participating cohorts’ MHC SNPs separately, retained overlapping variants with selected SNPs in 1KG, and cross-imputed each cohort’s missing variants by using 1KG genotypes. We finally concatenate all cohorts together to construct scaffold variants for multi-ancestry reference panel.

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