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Defining the clonality of peripheral T cell lymphomas using RNA-seq
- Source :
- Bioinformatics
- Publication Year :
- 2016
- Publisher :
- Oxford University Press (OUP), 2016.
-
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 (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 Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- 0301 basic medicine
Statistics and Probability
Receptors, Antigen, T-Cell, alpha-beta
T-Lymphocytes
T cell
Population
Clone (cell biology)
Biology
Biochemistry
Immunophenotyping
Flow cytometry
03 medical and health sciences
Antigen
Cell Line, Tumor
medicine
Humans
Cytotoxic T cell
Discovery Notes
education
Molecular Biology
education.field_of_study
Base Sequence
medicine.diagnostic_test
Sequence Analysis, RNA
T-cell receptor
Lymphoma, T-Cell, Peripheral
Flow Cytometry
Molecular biology
Clone Cells
3. Good health
Computer Science Applications
Computational Mathematics
030104 developmental biology
medicine.anatomical_structure
Computational Theory and Mathematics
Sequence Analysis
Subjects
Details
- ISSN :
- 13674811 and 13674803
- Volume :
- 33
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....b880726308c77bd58b20eb0498331519