Defining the clonality of peripheral T cell lymphomas using RNA-seq.
Bioinformatics
; 33(8): 1111-1115, 2017 04 15.
Article
em En
| MEDLINE
| ID: mdl-28003262
ABSTRACT
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 (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. 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.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Linfoma de Células T Periférico
/
Análise de Sequência de RNA
Limite:
Humans
Idioma:
En
Ano de publicação:
2017
Tipo de documento:
Article