Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing

(2018) Deng Pan et al.   SCIENCE

Genomic Biomarkers of a Randomized Trial Comparing First-line Everolimus and Sunitinib in Patients with Metastatic Renal Cell Carcinoma

(2017) James J. Hsieh et al.   EUROPEAN UROLOGY

Inactivation of the PBRM1 tumor suppressor gene amplifies the HIF-response in VHL−/−clear cell renal carcinoma

(2017) Wenhua Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

The SWI/SNF Protein PBRM1 Restrains VHL-Loss-Driven Clear Cell Renal Cell Carcinoma

(2017) Amrita M. Nargund et al.   Cell Reports

Immunomodulatory Activity of Nivolumab in Metastatic Renal Cell Carcinoma

(2016) Toni K. Choueiri et al.   CLINICAL CANCER RESEARCH

Mutations in TSC1, TSC2, and MTOR Are Associated with Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma

(2016) D. J. Kwiatkowski et al.   CLINICAL CANCER RESEARCH

Whole-Exome Sequencing in Two Extreme Phenotypes of Response to VEGF-Targeted Therapies in Patients With Metastatic Clear Cell Renal Cell Carcinoma

(2016) Andre P. Fay et al.   Journal of the National Comprehensive Cancer Network

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial

(2016) Jonathan E Rosenberg et al.   LANCET

Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

(2016) Valsamo Anagnostou et al.   Cancer Discovery

Tumor Mutational Load and Immune Parameters across Metastatic Renal Cell Carcinoma Risk Groups

(2016) G. de Velasco et al.   Cancer Immunology Research

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

(2015) Michael S. Rooney et al.   CELL

Molecular Subtypes of Clear Cell Renal Cell Carcinoma Are Associated with Sunitinib Response in the Metastatic Setting

(2015) B. Beuselinck et al.   CLINICAL CANCER RESEARCH

Paired exome analysis of Barrett's esophagus and adenocarcinoma

(2015) Matthew D Stachler et al.   NATURE GENETICS

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

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

Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma

(2015) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

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

(2015) N. A. Rizvi et al.   SCIENCE

Decreased PBRM1 expression predicts unfavorable prognosis in patients with clear cell renal cell carcinoma

(2015) Soo Jeong Nam et al.   UROLOGIC ONCOLOGY-SEMINARS AND ORIGINAL INVESTIGATIONS

Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets

(2015) P. K. Brastianos et al.   Cancer Discovery

The growth rate of “clinically significant” renal cancer

(2015) Ofer N. Gofrit et al.   SpringerPlus

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(2014) Eliezer M Van Allen et al.   NATURE MEDICINE

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

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

Immune checkpoint blockade immunotherapy to activate anti-tumour T-cell immunity

(2013) Alan G. Ramsay   BRITISH JOURNAL OF HAEMATOLOGY

Adverse Outcomes in Clear Cell Renal Cell Carcinoma with Mutations of 3p21 Epigenetic Regulators BAP1 and SETD2: A Report by MSKCC and the KIRC TCGA Research Network

(2013) A. A. Hakimi et al.   CLINICAL CANCER RESEARCH

Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation

(2013) Payal Kapur et al.   LANCET ONCOLOGY

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

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

(2013) Michael S. Lawrence et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Integrated molecular analysis of clear-cell renal cell carcinoma

(2013) Yusuke Sato et al.   NATURE GENETICS

Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

(2013) Cigall Kadoch et al.   NATURE GENETICS

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Loss of PBRM1 expression is associated with renal cell carcinoma progression

(2012) Rafal Pawłowski et al.   INTERNATIONAL JOURNAL OF CANCER

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

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

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

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

(2011) Ignacio Varela et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

Guidelines for the Evaluation of Immune Therapy Activity in Solid Tumors: Immune-Related Response Criteria

(2009) J. D. Wolchok et al.   CLINICAL CANCER RESEARCH

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

New response evaluation criteria in solid tumours: Revised RECIST guideline (version 1.1)

(2008) E.A. Eisenhauer et al.   EUROPEAN JOURNAL OF CANCER