hla typing from rna-seq sequence reads

we present a method, seq2hla, for obtaining an individual’s human leukocyte antigen (hla) class i and ii typeand expression using standard next generation sequencing rna-seq data. rna-seq reads are mapped against areference database of hla alleles, and hla type, confidence score and locus-specific expression level aredetermined. 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 expressionfor previously un-typed illumina body map tissues and a cohort of korean patients with lung cancer. because thealgorithm uses standard rna-seq reads and requires no change to laboratory protocols, it can be used for bothexisting datasets and future studies, thus adding a new dimension for hla typing and biomarker studies.