Determining patient HLA type via standard NGS data

Mainz, Germany, January 7, 2013 – TRON scientists have created a new computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future RNA-Seq reads. The method has been published in the December issue of Genome Medicine. The authors provide a tool which uses standard RNA-Seq reads and requires no change to lab protocols, adding a new dimension for HLA typing and biomarker studies.

The main task of the immune system is to protect the body against pathogenic influences from the outside, such as bacteria or viruses and from the inside, such as tumor-genesis. Human leukocyte antigens (HLA) play a central role in this task as they present peptides to the immune cells, which are derived either from normal self-proteins in a healthy condition, from pathogens in case of an infection or from abnormal self-proteins. “The NGS RNA-Seq protocol has been rapidly adopted worldwide to profile gene expression”, says the paper’s first author Sebastian Boegel of TRON. “Here, we show that the sequence reads derived from deep sequencing the transcriptome using standard NGS RNA-Seq can be further used both for existing and future datasets to determine the HLA type and expression. We foresee extensive synergies and improvements resulting from feedback between seq2HLA and increased NGS read length, increased NGS read accuracy, larger datasets, and increased reference HLA sequence databases.”