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Citation Context ...s, then multiplied by the number of clusters that contained two individuals (n = 1457) to correct for multiple testing to give the adjusted P value. Data analysis All data analysis was performed in R =-=[25]-=- v3.1.2 or Python (http://www.python.org) v2.4.3 and v3.2.2. Code availability Custom code is available upon request. Results and discussion Somatically rearranged T cell receptor sequences can be eff... |
| 303 |
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome,”
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Citation Context ...on of immune-related genes, all available RNASeqV2 data from the TCGA Data Portal were downloaded. These data provide gene expression information generated using MapSplice [20] for alignment and RSEM =-=[21]-=- to quantify gene expression. The reported scaled_estimate value was multiplied by 106 to obtain transcripts per million (TPM). To obtain consensus gene expression values, we summed the TPM values wit... |
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Clustering of highly homologous sequences to reduce the size of large protein databases
- Li, Jaroszewski, et al.
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Citation Context ...HC also shared a similar CDR3 sequence, we took all CDR3 sequences from all 1361 individuals, and clustered them to allow for inexact CDR3 sequence matches. We clustered at 95 % identity using CD-HIT =-=[23, 24]-=- v4.6 with the following parameters: −c 0.95; −n 5; −l 5. We then checked each cluster to see if it contained sequences from at least two individuals, and if those individuals shared a pMHC. We found ... |
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CD4 T cells are required to sustain CD8 cytotoxic T-cell responses during chronic viral infection.
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Citation Context ...d set of V and J gene primers [3]. TCR-seq applied to tissue specimens can provide insight into tumor-infiltrating lymphocytes [4, 5], T cells associated with autoimmune pathology [6–8] and infection =-=[9]-=-, * Correspondence: rholt@bcgsc.ca 1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada 2Genome Science and Technology Program, University of B... |
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Citation Context ...d beta chains are displayed in Additional file 1: Figure S1. For negative control RNA-seq data, we used pairedend 101-nucleotide RNA-seq data from seven TCRnegative cell lines, downloaded from ENCODE =-=[18]-=- and pooled for use as a negative control (Additional file 1: Table S1). To create negative datasets for shorter read lengths, reads from the 101-nucleotide datasets were truncated to 76-nucleotide an... |
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Tolerating some redundancy significantly speeds up clustering of large protein databases.
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Citation Context ...HC also shared a similar CDR3 sequence, we took all CDR3 sequences from all 1361 individuals, and clustered them to allow for inexact CDR3 sequence matches. We clustered at 95 % identity using CD-HIT =-=[23, 24]-=- v4.6 with the following parameters: −c 0.95; −n 5; −l 5. We then checked each cluster to see if it contained sequences from at least two individuals, and if those individuals shared a pMHC. We found ... |
| 43 |
et al: Intraepithelial CD8+ tumorinfiltrating lymphocytes and a high CD8+/regulatory T-cell ratio are associated with favorable prognosis in ovarian cancer
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Citation Context ...followed by 5′ rapid amplification of cDNA ends [2], or with a multiplexed set of V and J gene primers [3]. TCR-seq applied to tissue specimens can provide insight into tumor-infiltrating lymphocytes =-=[4, 5]-=-, T cells associated with autoimmune pathology [6–8] and infection [9], * Correspondence: rholt@bcgsc.ca 1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V... |
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Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, et al. Comprehensive assessment of T-cell receptor betachain diversity in alphabeta T cells. Blood 2009;114:4099–107
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Citation Context ...al T cells isolated from blood [1, 2]; amplifying the CDR3 region with a conserved C gene primer followed by 5′ rapid amplification of cDNA ends [2], or with a multiplexed set of V and J gene primers =-=[3]-=-. TCR-seq applied to tissue specimens can provide insight into tumor-infiltrating lymphocytes [4, 5], T cells associated with autoimmune pathology [6–8] and infection [9], * Correspondence: rholt@bcgs... |
| 29 |
Bufalino R, Zurrida S, Collini P, Cascinelli N. Prognostic value of tumor infiltrating lymphocytes in the vertical growth phase of primary cutaneous melanoma
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Citation Context ...followed by 5′ rapid amplification of cDNA ends [2], or with a multiplexed set of V and J gene primers [3]. TCR-seq applied to tissue specimens can provide insight into tumor-infiltrating lymphocytes =-=[4, 5]-=-, T cells associated with autoimmune pathology [6–8] and infection [9], * Correspondence: rholt@bcgsc.ca 1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V... |
| 23 |
Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res
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Citation Context ...is the main factor conferring T cell antigen specificity. Typically, CDR3 sequence information is acquired by performing TCR-sequencing (TCR-seq) experiments on peripheral T cells isolated from blood =-=[1, 2]-=-; amplifying the CDR3 region with a conserved C gene primer followed by 5′ rapid amplification of cDNA ends [2], or with a multiplexed set of V and J gene primers [3]. TCR-seq applied to tissue specim... |
| 23 |
Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res
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Citation Context ...1,056 reads; 2823 unique CDR3β sequences) and RNA-seq for total cDNA (56,067,687 reads; 9 unique CDR3β sequences) data from the same colorectal tumor tissue sample, using previously described methods =-=[12, 26]-=-. We observed that all high confidence CDR3βs identified by RNA-seq (n = 9) fell within the top 2.1 % (n = 60) of CDR3βs detected by TCR-seq, ranked by abundance (data not shown), confirming that at a... |
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SC, Kedl RM, et al. Naive CD4(+) T cell frequency varies for different epitopes and predicts repertoire diversity and response magnitude. Immunity (2007
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Citation Context ...itish Columbia, Vancouver, British Columbia V6T 1Z4, Canada Full list of author information is available at the end of the article and the properties of normal primary and secondary lymphatic tissues =-=[10, 11]-=-. Conventional TCR-seq methods provide a detailed view of TCR diversity [2, 3, 12]. However, because they rely on targeted amplicon sequencing, they do not evaluate TCR variation in the context of the... |
| 9 |
SJ, Huang Y, Savich GL, et al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res
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Citation Context ... diversity with the expression of immune-related genes, all available RNASeqV2 data from the TCGA Data Portal were downloaded. These data provide gene expression information generated using MapSplice =-=[20]-=- for alignment and RSEM [21] to quantify gene expression. The reported scaled_estimate value was multiplied by 106 to obtain transcripts per million (TPM). To obtain consensus gene expression values, ... |
| 9 | A et al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science 2014; 344 - Tran, Turcotte, et al. |
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EA et al. Neo-antigens predicted by tumor genome metaanalysis correlate with increased patient survival. Genome Res 2014
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Citation Context ...on-randomized data was taken as the P value. Shared peptide-MHC and CDR3 sequences We predicted HLA Class I alleles and MHC-presented point mutations for 1361 TCGA individuals as previously described =-=[22]-=-, with an IC50 value of 500 nM for MHC-predicted binding affinity taken as the maximum threshold for potential immunogenicity. We counted the frequency of each peptide-MHC (pMHC; n = 305,438), and fou... |
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Shugay M, Mamedov IZ, Putintseva EV, Turchaninova MA, Zvyagin IV, et al. MiTCR: software for T-cell receptor sequencing data analysis. Nat Methods (2013
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Citation Context ...able in this article, unless otherwise stated. Brown et al. Genome Medicines(2015) 7:125sDOI 10.1186/s13073-015-0248-x Extraction of T cell receptor CDR3 sequences from RNA-seq data We deployed MiTCR =-=[16]-=- v1.0.3, which is well suited for the annotation of CDR3 sequences from sequencing reads. However, upon initial application of MiTCR to tumor RNA-seq data using the default parameters, we identified h... |
| 6 |
Ribeca P, Raineri E, Lacroix V, Guigó R, et al. Modelling and simulating generic RNA-seq experiments with the flux simulator. Nucleic Acids Res
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Citation Context ... the V and J alignment parameters was selected. These optimal parameters are summarized in Additional file 1: Table S2. Benchmarking CDR3 extraction efficiency using simulated data The Flux Simulator =-=[19]-=- v1.2.1 is a computational tool that generates RNA-seq datasets by simulating a transcriptome expression profile, library construction, and sequencing errors. We simulated a range of sequencing depths... |
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et al. Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res (2011
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Citation Context ...information is available at the end of the article and the properties of normal primary and secondary lymphatic tissues [10, 11]. Conventional TCR-seq methods provide a detailed view of TCR diversity =-=[2, 3, 12]-=-. However, because they rely on targeted amplicon sequencing, they do not evaluate TCR variation in the context of the overall genetic diversity of the specimen from which the data are derived. Next-g... |
| 3 |
et al. Co-occurrence of anaerobic bacteria in colorectal carcinomas. Microbiome. 2013; 1: 16. doi: 10.1186/2049-2618-1-16 PMID: 24450771
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Citation Context ...erived RNA-seq datasets. Methods Ethics The research described herein conformed to the Helsinki Declaration. All clinical specimens not part of The Cancer Genome Atlas (TCGA) were obtained previously =-=[15]-=- with informed consent by the British Columbia Cancer Agency Tumor Tissue Repository, which operates as a dedicated biobank with approval from the University of British Columbia-British Columbia Cance... |
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Citation Context ...itish Columbia, Vancouver, British Columbia V6T 1Z4, Canada Full list of author information is available at the end of the article and the properties of normal primary and secondary lymphatic tissues =-=[10, 11]-=-. Conventional TCR-seq methods provide a detailed view of TCR diversity [2, 3, 12]. However, because they rely on targeted amplicon sequencing, they do not evaluate TCR variation in the context of the... |
| 1 |
Jūratė Šaltytė B, Holmøy T, et al. High-throughput sequencing of TCR repertoires in multiple sclerosis reveals intrathecal enrichment of EBV-reactive CD8+ T cells. Eur J Immunol. 2014;44: 3439–52. • We accept pre-submission inquiries • Our selector tool h
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Citation Context ...lls. Indeed, when we queried tumor-associated CDR3β sequences for matches to CDR3β sequences in the literature with defined antigen specificity, we found numerous matches to known viral-specific TCRs =-=[31]-=- (Fig. 4). TCGA CDR3βs with viral specificity were much more common within the set of shared TCGA CDR3βs than within the set of unique TCGA CDR3βs. Specifically, nine of 2197 CDR3βs Fig. 2 The number ... |
