title: HLA typing from RNA-Seq sequence reads.
abstract: We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen (HLA) class I and II type and expression using standard next generation sequencing RNA-Seq data. RNA-Seq reads are mapped against a reference database of HLA alleles, and HLA type, confidence score and locus-specific expression level are determined. We successfully applied seq2HLA to 50 individuals included in the HapMap project, yielding 100% specificity and 94% sensitivity at a P-value of 0.1 for two-digit HLA types. We determined HLA type and expression for previously un-typed Illumina Body Map tissues and a cohort of Korean patients with lung cancer. Because the algorithm uses standard RNA-Seq reads and requires no change to laboratory protocols, it can be used for both existing datasets and future studies, thus adding a new dimension for HLA typing and biomarker studies.
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany ; University Medical Center of the Johannes Gutenberg University Mainz, III, Medical Department, Langenbeckstrasse 1, 55131 Mainz, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Boegel
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Löwer
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany ; University Medical Center of the Johannes Gutenberg University Mainz, III, Medical Department, Langenbeckstrasse 1, 55131 Mainz, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Schäfer
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Bukur
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany.
authors.forename: Jos
authors.initials: J
authors.lastname: de Graaf
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany.
authors.forename: Valesca
authors.initials: V
authors.lastname: Boisguérin
authors.affiliation: Ganymed Pharmaceuticals AG, Freiligrathstrasse 12, 55131 Mainz, Germany.
authors.forename: Ozlem
authors.initials: O
authors.lastname: Türeci
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany.
authors.forename: Mustafa
authors.initials: M
authors.lastname: Diken
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany.
authors.forename: John C
authors.initials: JC
authors.lastname: Castle
authors.affiliation: TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany ; University Medical Center of the Johannes Gutenberg University Mainz, III, Medical Department, Langenbeckstrasse 1, 55131 Mainz, Germany.
authors.forename: Ugur
authors.initials: U
authors.lastname: Sahin