The gremlin in the works: why T cell receptor researchers need to pay more attention to germline reference sequences

This study relates insights borne out of years of studying TCRs, and interacting with the TCR research community. Published in collaboration with colleagues from the Adaptive Immune Receptor Repertoire Community (AIRR-C) re-analysing large public datasets, it details technical aspects of TCR analysis and reporting that I believe may be hindering TCR research interoperability and translation. Crucially, many TCRseq studies either do not cite a TCR germline reference, use an incorrect reference for their biological question, and take a prescriptive view of descriptive reference metadata that could be confounding their analyses.