title: Profiling tissue-resident T cell repertoires by RNA sequencing.
abstract: Deep sequencing of recombined T cell receptor (TCR) genes and transcripts has provided a view of T cell repertoire diversity at an unprecedented resolution. Beyond profiling peripheral blood, analysis of tissue-resident T cells provides further insight into immune-related diseases. We describe the extraction of TCR sequence information directly from RNA-sequencing data from 6738 tumor and 604 control tissues, with a typical yield of 1 TCR per 10 million reads. This method circumvents the need for PCR amplification of the TCR template and provides TCR information in the context of global gene expression, allowing integrated analysis of extensive RNA-sequencing data resources.
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: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada.|Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Raeburn
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada. rholt@bcgsc.ca.|Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada. rholt@bcgsc.ca.|Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada. rholt@bcgsc.ca.|Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada. rholt@bcgsc.ca.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Holt
mesh_terms: D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000276:immunology; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013601:T-Lymphocytes / Q000276:immunology
chemical_list: D011948:Receptors, Antigen, T-Cell