{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:53:33Z","timestamp":1760709213253,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,1,18]],"date-time":"2017-01-18T00:00:00Z","timestamp":1484697600000},"content-version":"vor","delay-in-days":28,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"British Columbia Cancer Foundation","award":["212SEQ"],"award-info":[{"award-number":["212SEQ"]}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["CIHR; MOP-102679"],"award-info":[{"award-number":["CIHR; MOP-102679"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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\u2019s 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>R scripts used in the processing of the data are available online at https:\/\/www.github.com\/scottdbrown\/RNAseq-TcellClonality<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw810","type":"journal-article","created":{"date-parts":[[2016,12,15]],"date-time":"2016-12-15T22:11:40Z","timestamp":1481839900000},"page":"1111-1115","source":"Crossref","is-referenced-by-count":11,"title":["Defining the clonality of peripheral T cell lymphomas using RNA-seq"],"prefix":"10.1093","volume":"33","author":[{"given":"Scott D","family":"Brown","sequence":"first","affiliation":[{"name":"Canada\u2019s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada"},{"name":"Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada"}]},{"given":"Greg","family":"Hapgood","sequence":"additional","affiliation":[{"name":"Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada"}]},{"given":"Christian","family":"Steidl","sequence":"additional","affiliation":[{"name":"Centre for Lymphoid Cancer, Department of Lymphoid Cancer Research, British Columbia Cancer Agency, Vancouver, Canada"}]},{"given":"Andrew P","family":"Weng","sequence":"additional","affiliation":[{"name":"Terry Fox Laboratory and Department of Pathology, British Columbia Cancer Agency, Vancouver, Canada"}]},{"given":"Kerry J","family":"Savage","sequence":"additional","affiliation":[{"name":"Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada"}]},{"given":"Robert A","family":"Holt","sequence":"additional","affiliation":[{"name":"Canada\u2019s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada"},{"name":"Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada"},{"name":"Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada"}]}],"member":"286","published-online":{"date-parts":[[2016,12,21]]},"reference":[{"key":"2023020205004786500_btw810-B1","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nmeth.2555","article-title":"MiTCR: software for T-cell receptor sequencing data analysis","volume":"10","author":"Bolotin","year":"2013","journal-title":"Nat. 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