3 years ago

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA [Genetics]

Zhen Xuan Yeo, Cynthia Vierra-Green, Jason Piper, Suzanne Brewerton, Stephen Spellman, Marie Wong, Ewen F. Kirkness, Chao Xie, Sally Howard, Amalio Telenti, Richard H. Scheuermann, Ken Bloom, William H. Biggs, Tao Long, J. Craig Venter, Yaron Turpaz, Colleen Brady

The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99–100% four-digit typing accuracy for both class I and II HLA genes, taking only ∼3 min to process a 30× whole-genome BAM file on a desktop computer.

DOI: 10.1073/pnas.1707945114

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