HLA typing from RNA-Seq sequence reads.
Ontology highlight
ABSTRACT:
SUBMITTER: Boegel S
PROVIDER: S-EPMC4064318 | biostudies-literature | 2012
REPOSITORIES: biostudies-literature
Publications
HLA typing from RNA-Seq sequence reads.
Boegel Sebastian S Löwer Martin M Schäfer Michael M Bukur Thomas T de Graaf Jos J Boisguérin Valesca V Türeci Ozlem O Diken Mustafa M Castle John C JC Sahin Ugur U
Genome medicine 20121222 12
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 ...[more]
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