Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

(2019) Robert M. Samstein et al.   NATURE GENETICS

Revisiting immune escape in colorectal cancer in the era of immunotherapy

(2019) Marieke Erica Ijsselsteijn et al.   BRITISH JOURNAL OF CANCER

Context Matters - Consensus Molecular Subtypes of Colorectal Cancer as Biomarkers for Clinical Trials

(2019) E Fontana et al.   ANNALS OF ONCOLOGY

Transforming Growth Factor-β Signaling in Immunity and Cancer

(2019) Eduard Batlle et al.   IMMUNITY

Tumor-derived TGF-β inhibits mitochondrial respiration to suppress IFN-γ production by human CD4+ T cells

(2019) Sarah Dimeloe et al.   Science Signaling

Smad7 Controls Immunoregulatory PDL2/1-PD1 Signaling in Intestinal Inflammation and Autoimmunity

(2019) Lucien P. Garo et al.   Cell Reports

Recognition of human gastrointestinal cancer neoantigens by circulating PD-1+ lymphocytes

(2019) Alena Gros et al.   JOURNAL OF CLINICAL INVESTIGATION

TGFβ drives immune evasion in genetically reconstituted colon cancer metastasis

(2018) Daniele V. F. Tauriello et al.   NATURE

A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade

(2018) Daniela S. Thommen et al.   NATURE MEDICINE

Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer

(2018) Janos L. Tanyi et al.   Science Translational Medicine

Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors

(2018) Thomas Duhen et al.   Nature Communications

Sensitive and frequent identification of high avidity neo-epitope specific CD8+ T cells in immunotherapy-naive ovarian cancer

(2018) Sara Bobisse et al.   Nature Communications

Cancer immunotherapy: broadening the scope of targetable tumours

(2018) Jitske van den Bulk et al.   Open Biology

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2018) Freddie Bray et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates

(2018) Yannick Simoni et al.   NATURE

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

(2018) Sanjeev Mariathasan et al.   NATURE

Actively personalized vaccination trial for newly diagnosed glioblastoma

(2018) Norbert Hilf et al.   NATURE

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

(2018) Derin B. Keskin et al.   NATURE

Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers

(2018) Wouter Scheper et al.   NATURE MEDICINE

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

(2017) Peter W. Eide et al.   Scientific Reports

Impaired T cell function in malignant pleural effusion is caused by TGF-β derived predominantly from macrophages

(2016) Lifeng Li et al.   INTERNATIONAL JOURNAL OF CANCER

Neoantigen landscape dynamics during human melanoma–T cell interactions

(2016) Els M. E. Verdegaal et al.   NATURE

Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

(2016) Alena Gros et al.   NATURE MEDICINE

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

(2016) Eric Tran et al.   NEW ENGLAND JOURNAL OF MEDICINE

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

Stromal gene expression defines poor-prognosis subtypes in colorectal cancer

(2015) Alexandre Calon et al.   NATURE GENETICS

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

Cancer Immunotherapy Based on Mutation-Specific CD4+ T Cells in a Patient with Epithelial Cancer

(2014) E. Tran et al.   SCIENCE

Transforming Growth Factor-β Signaling Controls the Formation and Maintenance of Gut-Resident Memory T Cells by Regulating Migration and Retention

(2013) Nu Zhang et al.   IMMUNITY

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

(2013) Nienke van Rooij et al.   JOURNAL OF CLINICAL ONCOLOGY

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS