RNA2HLA – HLA-based quality control of RNA-Seq datasets

RNA-sequencing (RNA-seq) is a widely used approach for accessing the transcriptome in biomedical research. Studies frequently include multiple samples taken from the same individual at various time points or under different conditions, correct assignment of those samples to each particular participant is evidently of great importance. Here, University of Oxford researchers propose taking advantage of typing the highly polymorphic genes from the human leukocyte antigen (HLA) complex in order to verify the correct allocation of RNA-seq samples to individuals. They have developed RNA2HLA, a novel quality control (QC) tool for performing study-wide HLA-typing for RNA-seq data and thereby identifying the samples from the common source. RNA2HLA allows precise allocation and grouping of RNA samples based on their HLA types. Strikingly, RNA2HLA revealed wrongly assigned samples from publicly available datasets and thereby demonstrated the importance of this tool for the quality control of RNA-seq studies. In addition, this tool successfully extracts HLA alleles in four-digital resolution and can be used to perform massive HLA-typing from RNA-seq based studies, which will serve multiple research purposes beyond sample QC.

RNA2HLA workflow

RNA2HLA workflow.

Availability – Project home page: https://github.com/Chelysheva/RNA2HLA

Chelysheva I, Pollard AJ, O’Connor D. (2021) RNA2HLA: HLA-based quality control of RNA-seq datasets. Brief Bioinform [Epub ahead of print]. [article]

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