| We present a method, seq2HLA, for obtaining an individualXs HLA class I and II type and expression using standard NGS RNA-Seq data. It comprises mapping RNA-Seq reads against a reference database of HLA alleles, determining and reporting HLA type, confidence score and locus-specific expression level. We successfully applied seq2HLA to 50 CEU HapMap individuals previously HLA-typed, yielding 100X specificity and 94X sensitivity at a p-value of 0.1 for 2-digit HLA types. We determine HLA-type and expression for the previously un-typed Illumina Bbody Mmap tissues and a cohort of Korean lung cancer patients. Because the algorithm uses standard RNA-Seq reads and requires no change to lab protocols, it can be used for both existing datasets and future studies, thus adding a new dimension for HLA typing and biomarker studies.
Citation: Boegel S, Lower M, Schafer M, Bukur T, de GJ, Boisguerin V, Tureci O, Diken M, Castle JC, Sahin U: HLA typing from RNA-Seq sequence reads. Genome Med 2012, 4:102 Links: http://genomemedicine.com/content/4/12/102/abstract http://www.ncbi.nlm.nih.gov/pubmed/23259685 doi:10.1186/gm403 |
hg clone https://toolshed.g2.bx.psu.edu/repos/sebastian-boegel/seq2hla
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| HLA typing from RNA-Seq sequence read | 1.0.0 | any | |