Defining the clonality of peripheral T cell lymphomas using RNA-seq

Motivation: In T‐cell lymphoma, malignant T cells arising from a founding clone share an identical T cell receptor (TCR) and can be identified by the over‐representation of this TCR relative to TCRs from the patient's repertoire of normal T cells. Here, we demonstrate that TCR information extracted from RNA‐seq data can provide a higher resolution view of peripheral T cell lymphomas (PTCLs) than that provided by conventional methods. Results: For 60 subjects with PTCL, flow cytometry/FACS was used to identify and sort aberrant T cell populations from diagnostic lymph node cell suspensions. For samples that did not appear to contain aberrant T cell populations, T helper (TH), T follicular helper (TFH) and cytotoxic T lymphocyte (CTL) subsets were sorted. RNA‐seq was performed on sorted T cell populations, and TCR alpha and beta chain sequences were extracted and quantified directly from the RNA‐seq data. 96% of the immunophenotypically aberrant samples had a dominant T cell clone readily identifiable by RNA‐seq. Of the samples where no aberrant population was found by flow cytometry, 80% had a dominant clone by RNA‐seq. This demonstrates the increased sensitivity and diagnostic ability of RNA‐seq over flow cytometry and shows that the presence of a normal immunophenotype does not exclude clonality. Availability and Implementation: R scripts used in the processing of the data are available online at https://www.github.com/scottdbrown/RNAseq‐TcellClonality Contacts: rholt@bcgsc.ca or ksavage@bccancer.bc.ca Supplementary information: Supplementary data are available at Bioinformatics online.