Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

Loss of IFN-γ Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-CTLA-4 Therapy

(2016) Jianjun Gao et al.   CELL

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

Combination Cancer Therapies with Immune Checkpoint Blockade: Convergence on Interferon Signaling

(2016) Andy J. Minn et al.   CELL

Potentiating the antitumour response of CD8+ T cells by modulating cholesterol metabolism

(2016) Wei Yang et al.   NATURE

Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma

(2016) Jesse M. Zaretsky et al.   NEW ENGLAND JOURNAL OF MEDICINE

Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade

(2016) P.-L. Chen et al.   Cancer Discovery

Biomarkers in Cancer Immunotherapy

(2015) Ton N. Schumacher et al.   CANCER CELL

Abstract 1307: Assessment of gene expression in peripheral blood from patients with advanced melanoma using RNA-seq before and after treatment with anti-PD-1 therapy with pembrolizumab (MK-3475)

(2015) Mark D. Ayers et al.   CANCER RESEARCH

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses

(2015) Ping-Chih Ho et al.   CELL

Metabolic Competition in the Tumor Microenvironment Is a Driver of Cancer Progression

(2015) Chih-Hao Chang et al.   CELL

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

Differential Expression of Immune-Regulatory Genes Associated with PD-L1 Display in Melanoma: Implications for PD-1 Pathway Blockade

(2015) J. M. Taube et al.   CLINICAL CANCER RESEARCH

Immunogenic peptide discovery in cancer genomes

(2015) Alexandra Snyder et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

TIGIT and PD-1 impair tumor antigen–specific CD8+ T cells in melanoma patients

(2015) Joe-Marc Chauvin et al.   JOURNAL OF CLINICAL INVESTIGATION

Pooled Analysis of Long-Term Survival Data From Phase II and Phase III Trials of Ipilimumab in Unresectable or Metastatic Melanoma

(2015) Dirk Schadendorf et al.   JOURNAL OF CLINICAL ONCOLOGY

Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity

(2015) Stefani Spranger et al.   NATURE

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

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

The Genetic Evolution of Melanoma from Precursor Lesions

(2015) A. Hunter Shain et al.   NEW ENGLAND JOURNAL OF MEDICINE

Combined Nivolumab and Ipilimumab or Monotherapy in Untreated Melanoma

(2015) James Larkin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

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

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

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

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

(2015) N. A. Rizvi et al.   SCIENCE

Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy

(2015) W. Peng et al.   Cancer Discovery

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

(2015) Mihaela Angelova et al.   GENOME BIOLOGY

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

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

The Immunoreceptor TIGIT Regulates Antitumor and Antiviral CD8 + T Cell Effector Function

(2014) Robert J. Johnston et al.   CANCER CELL

Chromosome 10, Frequently Lost in Human Melanoma, Encodes Multiple Tumor-Suppressive Functions

(2014) Lawrence N. Kwong et al.   CANCER RESEARCH

MPDL3280A (anti-PD-L1) treatment leads to clinical activity in metastatic bladder cancer

(2014) Thomas Powles et al.   NATURE

Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients

(2014) Roy S. Herbst et al.   NATURE

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

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

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

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

(2014) Christopher A. Miller et al.   PLoS Computational Biology

EXPANDS: expanding ploidy and allele frequency on nested subpopulations

(2013) Noemi Andor et al.   BIOINFORMATICS

The Continuum of Cancer Immunosurveillance: Prognostic, Predictive, and Mechanistic Signatures

(2013) Jérôme Galon et al.   IMMUNITY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Safety and Tumor Responses with Lambrolizumab (Anti–PD-1) in Melanoma

(2013) Omid Hamid et al.   NEW ENGLAND JOURNAL OF MEDICINE

Nivolumab plus Ipilimumab in Advanced Melanoma

(2013) Jedd D. Wolchok et al.   NEW ENGLAND JOURNAL OF MEDICINE

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

(2013) Chang Liu et al.   NUCLEIC ACIDS RESEARCH

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Using synthetic templates to design an unbiased multiplex PCR assay

(2013) Christopher S. Carlson et al.   Nature Communications

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

Tim-3/galectin-9 signaling pathway mediates T-cell dysfunction and predicts poor prognosis in patients with hepatitis B virus-associated hepatocellular carcinoma

(2012) Hang Li et al.   HEPATOLOGY

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

(2012) Hirokazu Matsushita et al.   NATURE

Expression of tumour-specific antigens underlies cancer immunoediting

(2012) Michel DuPage et al.   NATURE

Safety, Activity, and Immune Correlates of Anti–PD-1 Antibody in Cancer

(2012) Suzanne L. Topalian et al.   NEW ENGLAND JOURNAL OF MEDICINE

TSGene: a web resource for tumor suppressor genes

(2012) Min Zhao et al.   NUCLEIC ACIDS RESEARCH

Colocalization of Inflammatory Response with B7-H1 Expression in Human Melanocytic Lesions Supports an Adaptive Resistance Mechanism of Immune Escape

(2012) J. M. Taube et al.   Science Translational Medicine

Immune Inhibitory Molecules LAG-3 and PD-1 Synergistically Regulate T-cell Function to Promote Tumoral Immune Escape

(2011) S.-R. Woo et al.   CANCER RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Targeting Tim-3 and PD-1 pathways to reverse T cell exhaustion and restore anti-tumor immunity

(2010) Kaori Sakuishi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Tumor-infiltrating NY-ESO-1–specific CD8+T cells are negatively regulated by LAG-3 and PD-1 in human ovarian cancer

(2010) Junko Matsuzaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

The immunologic constant of rejection

(2008) Ena Wang et al.   TRENDS IN IMMUNOLOGY