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HLA typing from RNA-Seq sequence reads

Sebastian Boegel12, Martin Löwer1, Michael Schäfer12, Thomas Bukur1, Jos de Graaf1, Valesca Boisguérin1, Özlem Türeci3, Mustafa Diken1, John C Castle1* and Ugur Sahin12*

Author Affiliations

1 TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Langenbeckstrasse 1, Building 708, 55131 Mainz, Germany

2 University Medical Center of the Johannes Gutenberg University Mainz, III, Medical Department, Langenbeckstrasse 1, 55131 Mainz, Germany

3 Ganymed Pharmaceuticals AG, Freiligrathstrasse 12, 55131 Mainz, Germany

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Genome Medicine 2012, 4:102  doi:10.1186/gm403

Published: 22 December 2012


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.