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HLA typing from RNA-Seq sequence reads

2012; BioMed Central; Volume: 4; Issue: 12 Linguagem: Inglês

10.1186/gm403

1756-994X

Sebastian Boegel, Martin Löwer, Michael K. E. Schäfer, Thomas Bukur, Jos de Graaf, Valesca Boisguérin, Özlem Türeci, Mustafa Diken, John C. Castle, Uğur Şahin,

Cancer-related molecular mechanisms research

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.