Multilevel genomics of colorectal cancers with microsatellite instability—clinical impact of JAK1 mutations and consensus molecular subtype 1

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

Effects of microsatellite instability on recurrence patterns and outcomes in colorectal cancers

(2016) Chang Gon Kim et al.   BRITISH JOURNAL OF CANCER

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

(2016) Willy Hugo et al.   CELL

Immune and Stromal Classification of Colorectal Cancer Is Associated with Molecular Subtypes and Relevant for Precision Immunotherapy

(2016) Etienne Becht et al.   CLINICAL CANCER RESEARCH

Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability

(2016) Bernhard Mlecnik et al.   IMMUNITY

Classification and characterization of microsatellite instability across 18 cancer types

(2016) Ronald J Hause et al.   NATURE MEDICINE

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

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

Primary Resistance to PD-1 Blockade Mediated by JAK1/2 Mutations

(2016) Daniel Sanghoon Shin et al.   Cancer Discovery

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

(2016) Marios Giannakis et al.   Cell Reports

Regulator of Chromosome Condensation 2 Identifies High-Risk Patients within Both Major Phenotypes of Colorectal Cancer

(2015) J. Bruun et al.   CLINICAL CANCER RESEARCH

Four DNA methylation biomarkers in biliary brush samples accurately identify the presence of cholangiocarcinoma

(2015) Kim Andresen et al.   HEPATOLOGY

Differential DNA mismatch repair underlies mutation rate variation across the human genome

(2015) Fran Supek et al.   NATURE

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

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

A Big Bang model of human colorectal tumor growth

(2015) Andrea Sottoriva et al.   NATURE GENETICS

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity

(2015) Noemi Andor et al.   NATURE MEDICINE

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

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

Targeting JAK kinase in solid tumors: emerging opportunities and challenges

(2015) M Buchert et al.   ONCOGENE

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

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

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

(2014) S. D. Brown et al.   GENOME RESEARCH

Cancer incidence and mortality worldwide: Sources, methods and major patterns in GLOBOCAN 2012

(2014) Jacques Ferlay et al.   INTERNATIONAL JOURNAL OF CANCER

RNF43 is frequently mutated in colorectal and endometrial cancers

(2014) Marios Giannakis et al.   NATURE GENETICS

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

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

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

(2013) Beifang Niu et al.   BIOINFORMATICS

EXPANDS: expanding ploidy and allele frequency on nested subpopulations

(2013) Noemi Andor et al.   BIOINFORMATICS

A fast Peptide Match service for UniProt Knowledgebase

(2013) Chuming Chen et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes

(2013) Tae-Min Kim et al.   CELL

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

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

(2013) Kosuke Yoshihara et al.   Nature Communications

JAK1 truncating mutations in gynecologic cancer define new role of cancer-associated protein tyrosine kinase aberrations

(2013) Yuan Ren et al.   Scientific Reports

Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value

(2013) Laetitia Marisa et al.   PLOS MEDICINE

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Targeting the Interleukin-6/Jak/Stat Pathway in Human Malignancies

(2012) Pasquale Sansone et al.   JOURNAL OF CLINICAL ONCOLOGY

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

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

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

DNA Sequence Profiles of the Colorectal Cancer Critical Gene Set KRAS-BRAF-PIK3CA-PTEN-TP53 Related to Age at Disease Onset

(2010) Marianne Berg et al.   PLoS One

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

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

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Integrated detection and population-genetic analysis of SNPs and copy number variation

(2008) Steven A McCarroll et al.   NATURE GENETICS