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bioRxiv · 10.1101/035253

High-accuracy HLA type inference from whole-genome sequencing data

Alexander Dilthey·Pierre-Antoine Gourraud·Zamin Iqbal·Gil McVean
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Abstract

Extensive hyperpolymorphism and sequence similarity between the HLA genes make HLA type inference from whole-genome sequencing data a challenging problem. We address these by representing sequences from over 10,000 known alleles in a reference graph structure, enabling accurate read mapping. HLA*PRG, our algorithm, outperforms existing methods by a wide margin and for the first time consistently achieves the accuracy of gold-standard reference methods with one error across 158 alleles tested.

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Alexander Dilthey, Pierre-Antoine Gourraud, Zamin Iqbal, Gil McVean. 2015-12-24. High-accuracy HLA type inference from whole-genome sequencing data. https://doi.org/10.1101/035253

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