Immunogenomics of Colorectal Cancer Response to Checkpoint Blockade: Analysis of the KEYNOTE 177 Trial and Validation Cohorts

The association between tumor mutational burden and prognosis is dependent on treatment context

(2021) Cristina Valero et al.   NATURE GENETICS

A practical guide to cancer subclonal reconstruction from DNA sequencing

(2021) Maxime Tarabichi et al.   NATURE METHODS

CD4 T cell dependent rejection of beta 2 microglobulin null mismatch repair deficient tumors

(2021) Giovanni Germano et al.   Cancer Discovery

Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival

(2020) Mary A. Wood et al.   Genome Medicine

High PD-1/PD-L1 Checkpoint Interaction Infers Tumor Selection and Therapeutic Sensitivity to Anti-PD-1/PD-L1 Treatment

(2020) Lissete Sánchez-Magraner et al.   CANCER RESEARCH

Pembrolizumab in Microsatellite-Instability–High Advanced Colorectal Cancer

(2020) Thierry André et al.   NEW ENGLAND JOURNAL OF MEDICINE

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy

(2019) Imran Siddiqui et al.   IMMUNITY

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

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

Immunotherapy in colorectal cancer: rationale, challenges and potential

(2019) Karuna Ganesh et al.   Nature Reviews Gastroenterology & Hepatology

Tumor mutational burden is predictive of response to immune checkpoint inhibitors in MSI-high metastatic colorectal cancer

(2019) A B Schrock et al.   ANNALS OF ONCOLOGY

NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline

(2019) Ryan O. Schenck et al.   BMC BIOINFORMATICS

High-dimensional cytometric analysis of colorectal cancer reveals novel mediators of antitumour immunity

(2019) Natasja L de Vries et al.   GUT

Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma

(2019) Thanos P. Mourikis et al.   Nature Communications

An intra-tumoral niche maintains and differentiates stem-like CD8 T cells

(2019) Caroline S. Jansen et al.   NATURE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

Cancer immunotherapy using checkpoint blockade

(2018) Antoni Ribas et al.   SCIENCE

Genetic Mechanisms of Immune Evasion in Colorectal Cancer

(2018) Catherine S. Grasso et al.   Cancer Discovery

QuantSeq 3′ mRNA sequencing for RNA quantification

(2018) Pamela Moll et al.   NATURE METHODS

The Link between the Multiverse of Immune Microenvironments in Metastases and the Survival of Colorectal Cancer Patients

(2018) Marc Van den Eynde et al.   CANCER CELL

Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers

(2017) Aaron M. Goodman et al.   MOLECULAR CANCER THERAPEUTICS

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

(2017) Dung T. Le et al.   SCIENCE

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

(2017) Moshe Sade-Feldman et al.   Nature Communications

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

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

Comprehensive analysis of β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling

(2014) Andreas Herbst et al.   BMC GENOMICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

Using synthetic templates to design an unbiased multiplex PCR assay

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

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Improved Endpoints for Cancer Immunotherapy Trials

(2010) A. Hoos et al.   JNCI-Journal of the National Cancer Institute

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE