Reply to "Evaluation of immune repertoire inference methods from RNA-seq data"

Clinical and biological studies are often aimed at discovering a small fraction of T cell receptor (TCR) or immunoglobulin variants shared between samples or groups of samples—for example, when searching for the common clonotypes involved in response to tumor antigens, infectious agent antigens or self antigens1. In this context, even a single false intersection between immune repertoires extracted from different samples may compromise the utility of the results. Among the scientific community, complementarity-determining region 3 (CDR3) with designated V and J gene segments is the accepted identifier that unambiguously defines TCR alfa- or a beta-chain sequence.