ArcasHLA: high-resolution HLA typing from RNAseq.

ABSTRACT:

Motivation

The human leukocyte antigen (HLA) locus plays a critical role in tissue compatibility and regulates the host response to many diseases, including cancers and autoimmune di3orders. Recent improvements in the quality and accessibility of next-generation sequencing have made HLA typing from standard short-read data practical. However, this task remains challenging given the high level of polymorphism and homology between HLA genes. HLA typing from RNA sequencing is further complicated by post-transcriptional modifications and bias due to amplification.

Results

Here, we present arcasHLA: a fast and accurate in silico tool that infers HLA genotypes from RNA-sequencing data. Our tool outperforms established tools on the gold-standard benchmark dataset for HLA typing in

SUBMITTER: Orenbuch R 

PROVIDER: S-EPMC6956775 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature