Extended Data Fig. 5: Merging genotyped and sequenced variants across the HLA region for an imputation panel. | Nature Medicine

Extended Data Fig. 5: Merging genotyped and sequenced variants across the HLA region for an imputation panel.

From: High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response

Extended Data Fig. 5

The first stage in building an imputation panel involved merging variant calls defined through genotyping arrays or next-generation sequencing (NGS). To determine whether imputation calls would differ based on the origin of variant calls we compared imputation performance (using the original HLA*IMP:02 algorithm) in individuals from four African populations with variant data called by array genotyping (Array) or next-generation sequence data (NGS). Points are concordance estimates between imputed and MiSeq called HLA alleles for each gene locus. The box plot centre line represents the median; the box limits, the upper and lower quartiles; and the whiskers are the 1.5x interquartile range. ACB: African Caribbean in Barbados (n = 76); ASW: African Ancestry in Southwest USA (n = 59); LWK: Luhya in Webuye, Kenya (n = 97); YRI: Yoruba in Ibadan, Nigeria (n = 108).

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