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.


Data integration and computational workflow.


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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