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- Title
HLA typing from RNA-Seq sequence reads.
- Authors
Boegel, Sebastian; Löwer, Martin; Schäfer, Michael; Bukur, Thomas; De Graaf, Jos; Boisguérin, Valesca; Türeci, Özlem; Diken, Mustafa; Castle, John C; Sahin, Ugur
- 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.
- Subjects
HLA histocompatibility antigens; NUCLEOTIDE sequence; LUNG cancer; BIOMARKERS; GENE expression
- Publication
Genome Medicine, 2012, Vol 4, Issue 12, p1
- ISSN
1756-994X
- Publication type
Article
- DOI
10.1186/gm403