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.
Availability – https://bitbucket.org/sebastian_boegel/seq2hla