seq2HLA – In Silico HLA Typing Using Standard RNA-Seq Sequence Reads

Researchers from Johannes Gutenberg-University Medical Center have developed and continue to improve an algorithm, seq2HLA that uses RNA-Seq NGS sequence reads in conjunction with over 6,000 known HLA allele reference sequences. It utilizes an alignment-based approach to determine the 4-digit HLA class I and class II types, a confidence score, zygosity, and locus-specific expression levels.

Here, they describe how to use the method, seq2HLA, to quickly and easily determine HLA class I and II types as well as HLA expression from a sample using standard next-generation sequencing RNA-Seq sequence reads. As an example, they demonstrate how to retrieve RNA-Seq sequence reads of the human Burkitt lymphoma cell lines Raji from NCBI SRA and determine the HLA type and HLA expression.

rna-seq

Data integration and computational workflow.

Availabilityhttps://bitbucket.org/sebastian_boegel/seq2hla

Boegel S, Scholtalbers J, Löwer M, Sahin U, Castle JC. (2015) In Silico HLA Typing Using Standard RNA-Seq Sequence Reads. Methods Mol Biol 1310:247-58. [abstract]

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