Ontology highlight
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 terms of both accuracy and speed, with an accuracy rate of 100% at two-field resolution for Class I genes, and over 99.7% for Class II. Furthermore, we evaluate the performance of our tool on a new biological dataset of 447 single-end total RNA samples from nasopharyngeal swabs, and establish the applicability of arcasHLA in metatranscriptome studies.Availability and implementation
arcasHLA is available at https://github.com/RabadanLab/arcasHLA.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Orenbuch R
PROVIDER: S-EPMC6956775 | biostudies-literature | 2020 Jan
REPOSITORIES: biostudies-literature
Orenbuch Rose R Filip Ioan I Comito Devon D Shaman Jeffrey J Pe'er Itsik I Rabadan Raul R
Bioinformatics (Oxford, England) 20200101 1
<h4>Motivation</h4>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 compli ...[more]