title: In Silico HLA Typing Using Standard RNA-Seq Sequence Reads.
abstract: Next-generation sequencing (NGS) enables high-throughput transcriptome profiling using the RNA-Seq assay, resulting in billions of short sequence reads. Worldwide adoption has been rapid: many laboratories worldwide generate transcriptome sequence reads daily. Here, we describe methods for obtaining a sample's human leukocyte antigen (HLA) class I and II types and HLA expression using standard NGS RNA-Seq sequence reads. We demonstrate the application using our algorithm, seq2HLA, and a publicly available RNA-Seq dataset from the Burkitt lymphoma cell line Raji.
authors.affiliation: TRON gGmbH - Translational Oncology at Johannes Gutenberg-University Medical Center gGmbH Mainz, Langenbeckstr. 1, Building 708, Mainz, 55131, Germany, boegels@uni-mainz.de.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Boegel
authors.forename: Jelle
authors.initials: J
authors.lastname: Scholtalbers
authors.forename: Martin
authors.initials: M
authors.lastname: Löwer
authors.forename: Ugur
authors.initials: U
authors.lastname: Sahin
authors.forename: John C
authors.initials: JC
authors.lastname: Castle
mesh_terms: D002051:Burkitt Lymphoma / Q000235:genetics; D045744:Cell Line, Tumor; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D006680:HLA Antigens / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006650:Histocompatibility Testing / Q000379:methods*; D006801:Humans; D012313:RNA / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D006680:HLA Antigens; D012313:RNA