title: Defining the clonality of peripheral T cell lymphomas using RNA-seq.
abstract: 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.
  
  
  
  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 (T H ), T follicular helper (T FH ) 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.
  
  
  
  R scripts used in the processing of the data are available online at https://www.github.com/scottdbrown/RNAseq-TcellClonality.
  
  
  
  rholt@bcgsc.ca or ksavage@bccancer.bc.ca.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.|Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Scott D
authors.initials: SD
authors.lastname: Brown
authors.affiliation: Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada.
authors.forename: Greg
authors.initials: G
authors.lastname: Hapgood
authors.affiliation: Centre for Lymphoid Cancer, Department of Lymphoid Cancer Research, British Columbia Cancer Agency, Vancouver, Canada.
authors.forename: Christian
authors.initials: C
authors.lastname: Steidl
authors.affiliation: Terry Fox Laboratory and Department of Pathology, British Columbia Cancer Agency, Vancouver, Canada.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Weng
authors.affiliation: Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada.
authors.forename: Kerry J
authors.initials: KJ
authors.lastname: Savage
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.|Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.|Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.|Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Holt
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D002999:Clone Cells; D005434:Flow Cytometry; D006801:Humans; D016130:Immunophenotyping; D016411:Lymphoma, T-Cell, Peripheral / Q000235:genetics* / Q000473:pathology*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D013601:T-Lymphocytes / Q000276:immunology
chemical_list: D016693:Receptors, Antigen, T-Cell, alpha-beta