ArticleScientific reports2016
Immune DNA signature of T-cell infiltration in breast tumor exomes.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- The case for caution in the application of whole-exome sequencing data for immune repertoire analysis.Briefings in bioinformatics · 2026Article
- Single-cell profiling reveals unique features of diabetogenic T cells in anti-PD-1-induced type 1 diabetes mice.The Journal of experimental medicine · 2023Article
- Adaptive immune receptor features related to breast cancer tissue in Kenyan patients: high immunoglobulin gene expression and high levels of gamma-delta T-cells.Breast cancer research and treatment · 2023Article
- TCR-sequencing in cancer and autoimmunity: barcodes and beyond.Trends in immunology · 2022Review
- Article
- Mutational profiling of micro-dissected pre-malignant lesions from archived specimens.BMC medical genomics · 2020Article
- Immunotyping of tumor-infiltrating lymphocytes in triple-negative breast cancer and genetic characterization.Oncology letters · 2020Article
- Clonotypic heterogeneity in cutaneous T-cell lymphoma (mycosis fungoides) revealed by comprehensive whole-exome sequencing.Blood advances · 2019Article
- Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue.Cancer research · 2019Article
- Recovery of T-cell receptor V(D)J recombination reads from lower grade glioma exome files correlates with reduced survival and advanced cancer grade.Journal of neuro-oncology · 2018Article
- Recovery of Immunoglobulin VJ Recombinations from Pancreatic Cancer Exome Files Strongly Correlates with Reduced Survival.Cancer microenvironment : official journal of the International Cancer Microenvironment Society · 2018Article
- Lung tumor exome files with T-cell receptor recombinations: a mouse model of T-cell infiltrates reflecting mutation burdens.Laboratory investigation; a journal of technical methods and pathology · 2017Article
- Informatics for cancer immunotherapy.Annals of oncology : official journal of the European Society for Medical Oncology · 2017Review
- T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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Authors and funding
8 authors.
Funding
Abstract
Tumor infiltrating lymphocytes (TILs) have been associated with favorable prognosis in multiple tumor types. The Cancer Genome Atlas (TCGA) represents the largest collection of cancer molecular data, but lacks detailed information about the immune environment. Here, we show that exome reads mapping to the complementarity-determining-region 3 (CDR3) of mature T-cell receptor beta (TCRB) can be used as an immune DNA (iDNA) signature. Specifically, we propose a method to identify CDR3 reads in a breast tumor exome and validate it using deep TCRB sequencing. In 1,078 TCGA breast cancer exomes, the fraction of CDR3 reads was associated with TILs fraction, tumor purity, adaptive immunity gene expression signatures and improved survival in Her2+ patients. Only 2/839 TCRB clonotypes were shared between patients and none associated with a specific HLA allele or somatic driver mutations. The iDNA biomarker enriches the comprehensive dataset collected through TCGA, revealing associations with other molecular features and clinical outcomes.
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