Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma

Mapping the immune environment in clear cell renal carcinoma by single-cell genomics

(2021) Nicholas Borcherding et al.   Communications Biology

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma

(2021) David A. Braun et al.   CANCER CELL

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

(2021) Kevin Bi et al.   CANCER CELL

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

(2021) Kevin Litchfield et al.   CELL

Open-Label, Single-Arm, Phase II Study of Pembrolizumab Monotherapy as First-Line Therapy in Patients With Advanced Non–Clear Cell Renal Cell Carcinoma

(2021) David F. McDermott et al.   JOURNAL OF CLINICAL ONCOLOGY

Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

(2021) Chirag Krishna et al.   CANCER CELL

Adjuvant Pembrolizumab after Nephrectomy in Renal-Cell Carcinoma

(2021) Toni K. Choueiri et al.   NEW ENGLAND JOURNAL OF MEDICINE

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

B cells are associated with survival and immunotherapy response in sarcoma

(2020) Florent Petitprez et al.   NATURE

B cells and tertiary lymphoid structures promote immunotherapy response

(2020) Beth A. Helmink et al.   NATURE

Checkpoint inhibitor immunotherapy in kidney cancer

(2020) Wenxin Xu et al.   Nature Reviews Urology

Phase and context shape the function of composite oncogenic mutations

(2020) Alexander N. Gorelick et al.   NATURE

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

(2020) Christopher R. Merritt et al.   NATURE BIOTECHNOLOGY

Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma

(2020) David A. Braun et al.   NATURE MEDICINE

The Evolutionary Origins of Recurrent Pancreatic Cancer

(2020) Hitomi Sakamoto et al.   Cancer Discovery

Mammalian SWI/SNF complex genomic alterations and immune checkpoint blockade in solid tumors

(2020) Sarah Abou Alaiwi et al.   Cancer Immunology Research

Escape from nonsense-mediated decay associates with anti-tumor immunogenicity

(2020) Kevin Litchfield et al.   Nature Communications

TOX is expressed by exhausted and polyfunctional human effector memory CD8+ T cells

(2020) Takuya Sekine et al.   Science Immunology

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

(2020) Pierre Barennes et al.   NATURE BIOTECHNOLOGY

Avelumab plus axitinib versus sunitinib in advanced renal cell carcinoma: biomarker analysis of the phase 3 JAVELIN Renal 101 trial

(2020) Robert J. Motzer et al.   NATURE MEDICINE

Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade

(2020) Robert J. Motzer et al.   CANCER CELL

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Avelumab plus Axitinib versus Sunitinib for Advanced Renal-Cell Carcinoma

(2019) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

(2019) Brian C. Miller et al.   NATURE IMMUNOLOGY

Neoantigen-directed immune escape in lung cancer evolution

(2019) Rachel Rosenthal et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection

(2019) Chen Yao et al.   NATURE IMMUNOLOGY

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

Updated European Association of Urology Guidelines on Renal Cell Carcinoma: Immune Checkpoint Inhibition Is the New Backbone in First-line Treatment of Metastatic Clear-cell Renal Cell Carcinoma

(2019) Laurence Albiges et al.   EUROPEAN UROLOGY

LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly

(2019) Jan Attig et al.   GENOME RESEARCH

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Clinical Validation of PBRM1 Alterations as a Marker of Immune Checkpoint Inhibitor Response in Renal Cell Carcinoma

(2019) David A. Braun et al.   JAMA Oncology

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

(2019) Kroopa Joshi et al.   NATURE MEDICINE

Clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

(2019) Thomas Powles et al.   NATURE MEDICINE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

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

(2019) Caroline S. Jansen et al.   NATURE

Epigenetic therapy of myelodysplastic syndromes connects to cellular differentiation independently of endogenous retroelement derepression

(2019) Anastasiya Kazachenka et al.   Genome Medicine

T Cell Dysfunction in Cancer

(2018) Daniela S. Thommen et al.   CANCER CELL

Tumor Mutational Burden and Efficacy of Nivolumab Monotherapy and in Combination with Ipilimumab in Small-Cell Lung Cancer

(2018) Matthew D. Hellmann et al.   CANCER CELL

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

(2018) Allen W. Zhang et al.   CELL

Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal

(2018) Samra Turajlic et al.   CELL

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

(2018) Samra Turajlic et al.   CELL

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

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma

(2018) David F. McDermott et al.   NATURE MEDICINE

Nivolumab plus Ipilimumab versus Sunitinib in Advanced Renal-Cell Carcinoma

(2018) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2018) Diana Miao et al.   SCIENCE

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

(2018) Thomas Duhen et al.   Nature Communications

Patterns of genomic evolution in advanced melanoma

(2018) E. Birkeland et al.   Nature Communications

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

(2018) Christopher J. Ricketts et al.   Cell Reports

High Densities of Tumor-Associated Plasma Cells Predict Improved Prognosis in Triple Negative Breast Cancer

(2018) Joe Yeong et al.   Frontiers in Immunology

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

(2018) Yannick Simoni et al.   NATURE

Fundamental Mechanisms of Immune Checkpoint Blockade Therapy

(2018) Spencer C. Wei et al.   Cancer Discovery

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

(2018) Hanjie Li et al.   CELL

Evolution of Metastases in Space and Time under Immune Selection

(2018) Mihaela Angelova et al.   CELL

Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma

(2018) Christof C. Smith et al.   JOURNAL OF CLINICAL INVESTIGATION

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Renal Cell Carcinoma (RCC) Tumors Display Large Expansion of Double Positive (DP) CD4+CD8+ T Cells With Expression of Exhaustion Markers

(2018) Laurence C. Menard et al.   Frontiers in Immunology

Evolving adoptive cellular therapies in urological malignancies

(2017) Yien Ning Sophia Wong et al.   LANCET ONCOLOGY

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

(2017) Alexander C. Huang et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

The immune contexture in cancer prognosis and treatment

(2017) Wolf H. Fridman et al.   Nature Reviews Clinical Oncology

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

(2017) Dung T. Le et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer

(2017) Scott Gettinger et al.   Cancer Discovery

Physiological and Pathological Transcriptional Activation of Endogenous Retroelements Assessed by RNA-Sequencing of B Lymphocytes

(2017) Jan Attig et al.   Frontiers in Microbiology

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

(2017) Theres Oakes et al.   Frontiers in Immunology

Biomarkers for immunotherapy in bladder cancer: a moving target

(2017) David H. Aggen et al.   Journal for ImmunoTherapy of Cancer

Gene expression markers of Tumor Infiltrating Leukocytes

(2017) Patrick Danaher et al.   Journal for ImmunoTherapy of Cancer

Cancer incidence and mortality projections in the UK until 2035

(2016) C R Smittenaar et al.   BRITISH JOURNAL OF CANCER

Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer

(2016) Elena Cherkasova et al.   CANCER RESEARCH

Tumor-Infiltrating Plasma Cells Are Associated with Tertiary Lymphoid Structures, Cytolytic T-Cell Responses, and Superior Prognosis in Ovarian Cancer

(2016) D. R. Kroeger et al.   CLINICAL CANCER RESEARCH

Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis

(2016) Andrea Schietinger et al.   IMMUNITY

Prognostic impact of tumour-infiltrating B cells and plasma cells in colorectal cancer

(2016) Jonna Berntsson et al.   INTERNATIONAL JOURNAL OF CANCER

Indel variant analysis of short-read sequencing data with Scalpel

(2016) Han Fang et al.   Nature Protocols

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

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

Classification and characterization of human endogenous retroviruses; mosaic forms are common

(2016) Laura Vargiu et al.   Retrovirology

Evidence of intermetastatic heterogeneity for pathological response and genetic mutations within colorectal liver metastases following preoperative chemotherapy

(2016) Mylène Sebagh et al.   Oncotarget

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits

(2016) Hai Fang et al.   Genome Medicine

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Intra-patient Inter-metastatic Genetic Heterogeneity in Colorectal Cancer as a Key Determinant of Survival after Curative Liver Resection

(2016) Anita Sveen et al.   PLoS Genetics

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

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

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

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

(2015) Michael S. Rooney et al.   CELL

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

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

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

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

(2015) N. A. Rizvi et al.   SCIENCE

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

(2015) Katharine Best et al.   Scientific Reports

Systematic Evaluation of the Prognostic Impact and Intratumour Heterogeneity of Clear Cell Renal Cell Carcinoma Biomarkers

(2014) Sakshi Gulati et al.   EUROPEAN UROLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

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

(2014) Marco Gerlinger et al.   NATURE GENETICS

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

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

Copy Number Loss of the Interferon Gene Cluster in Melanomas Is Linked to Reduced T Cell Infiltrate and Poor Patient Prognosis

(2014) Peter S. Linsley et al.   PLoS One

Improved Survival with T Cell Clonotype Stability After Anti-CTLA-4 Treatment in Cancer Patients

(2014) E. Cha et al.   Science Translational Medicine

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine

(2013) N. Thomas et al.   BIOINFORMATICS

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

(2013) Gro Nilsen et al.   BMC GENOMICS

CD137 Accurately Identifies and Enriches for Naturally Occurring Tumor-Reactive T Cells in Tumor

(2013) Q. Ye et al.   CLINICAL CANCER RESEARCH

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Parent-specific copy number in paired tumor–normal studies using circular binary segmentation

(2011) Adam B. Olshen et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

A revised nomenclature for transcribed human endogenous retroviral loci

(2011) Jens Mayer et al.   Mobile DNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Differentiation and Persistence of Memory CD8+ T Cells Depend on T Cell Factor 1

(2010) Xinyuan Zhou et al.   IMMUNITY

Phase I Study of Single-Agent Anti–Programmed Death-1 (MDX-1106) in Refractory Solid Tumors: Safety, Clinical Activity, Pharmacodynamics, and Immunologic Correlates

(2010) Julie R. Brahmer et al.   JOURNAL OF CLINICAL ONCOLOGY

A pilot clinical trial testing mutant von Hippel-Lindau peptide as a novel immune therapy in metastatic Renal Cell Carcinoma

(2010) Osama E Rahma et al.   Journal of Translational Medicine

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

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

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Microsatellite instability and hMLH1 and hMSH2 expression in renal tumors

(2010) Altavilla   ONCOLOGY REPORTS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Patterns of Gene Expression and Copy-Number Alterations in von-Hippel Lindau Disease-Associated and Sporadic Clear Cell Carcinoma of the Kidney

(2009) R. Beroukhim et al.   CANCER RESEARCH

Prognostic Factors for Overall Survival in Patients With Metastatic Renal Cell Carcinoma Treated With Vascular Endothelial Growth Factor–Targeted Agents: Results From a Large, Multicenter Study

(2009) Daniel Y.C. Heng et al.   JOURNAL OF CLINICAL ONCOLOGY

High‐dose interleukin‐2 for the treatment of metastatic renal cell carcinoma

(2008) Jacob A. Klapper et al.   CANCER

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

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Regression of human kidney cancer following allogeneic stem cell transplantation is associated with recognition of an HERV-E antigen by T cells

(2008) Yoshiyuki Takahashi et al.   JOURNAL OF CLINICAL INVESTIGATION