Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

B cells are associated with survival and immunotherapy response in sarcoma

(2020) Florent Petitprez et al.   NATURE

A genome-wide transcriptomic analysis of protein-coding genes in human blood cells

(2020) Mathias Uhlen et al.   SCIENCE

Molecular profiling for precision cancer therapies

(2020) Eoghan R. Malone et al.   Genome Medicine

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

Baseline Frequency of Inflammatory Cxcl9-Expressing Tumor-Associated Macrophages Predicts Response to Avelumab Treatment

(2020) Yan Qu et al.   Cell Reports

Approaches to treat immune hot, altered and cold tumours with combination immunotherapies

(2019) Jérôme Galon et al.   NATURE REVIEWS DRUG DISCOVERY

Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics

(2019) Pawel Suwinski et al.   Frontiers in Genetics

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Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy

(2019) Tuba N. Gide et al.   CANCER CELL

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

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Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial

(2019) Jordi Rodon et al.   NATURE MEDICINE

Nrf2 in cancers: A double‐edged sword

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The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom

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Cancer-associated fibroblasts: an emerging target of anti-cancer immunotherapy

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Integrated genomic profiling expands clinical options for patients with cancer

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EXTH-12. RADIATION ENHANCES MELANOMA RESPONSE TO IMMUNOTHERAPY AND SYNERGIZES WITH BENZODIAZEPINES TO PROMOTE ANTI-TUMOR ACTIVITY

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DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load

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Development and validation of a targeted gene sequencing panel for application to disparate cancers

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Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

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Oncogenic Signaling Pathways in The Cancer Genome Atlas

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The Immune Landscape of Cancer

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Immune Cell Infiltration and Tertiary Lymphoid Structures as Determinants of Antitumor Immunity

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Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer

(2018) Seung Tae Kim et al.   NATURE MEDICINE

RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas

(2018) Manfred Kunz et al.   ONCOGENE

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

(2018) Deng Pan et al.   SCIENCE

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

(2018) Diana Miao et al.   SCIENCE

MHC proteins confer differential sensitivity to CTLA-4 and PD-1 blockade in untreated metastatic melanoma

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Defining the role of the tumor vasculature in antitumor immunity and immunotherapy

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Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

(2018) Joel Saltz et al.   Cell Reports

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

(2018) Kyle Ellrott et al.   Cell Systems

Added Value of Whole-Exome and Transcriptome Sequencing for Clinical Molecular Screenings of Advanced Cancer Patients With Solid Tumors

(2018) Florence Koeppel et al.   CANCER JOURNAL

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

(2018) Sanjeev Mariathasan et al.   NATURE

Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma

(2018) Noam Auslander et al.   NATURE MEDICINE

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(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy

(2018) Razvan Cristescu et al.   SCIENCE

TGF-β-associated extracellular matrix genes link cancer-associated fibroblasts to immune evasion and immunotherapy failure

(2018) Ankur Chakravarthy et al.   Nature Communications

Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma

(2017) Winnie S. Liang et al.   GENOME RESEARCH

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

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Integrated genomic characterization of oesophageal carcinoma

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(2017) Dan R. Robinson et al.   NATURE

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

(2017) Marta Łuksza et al.   NATURE

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(2017) Nicholas K. Hayward et al.   NATURE

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

Cancer transcriptome profiling at the juncture of clinical translation

(2017) Marcin Cieślik et al.   NATURE REVIEWS GENETICS

Overall Survival with Combined Nivolumab and Ipilimumab in Advanced Melanoma

(2017) Jedd D. Wolchok et al.   NEW ENGLAND JOURNAL OF MEDICINE

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy

(2017) Diego Chowell et al.   SCIENCE

Cancer associated fibroblasts: An essential role in the tumor microenvironment

(2017) Leilei Tao et al.   Oncology Letters

Genomic landscape associated with potential response to anti-CTLA-4 treatment in cancers

(2017) Chan-Young Ock et al.   Nature Communications

Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

(2017) Martin Lauss et al.   Nature Communications

A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape

(2017) Elisabeth Castellanos et al.   Scientific Reports

Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression

(2017) Angel Garcia-Diaz et al.   Cell Reports

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

(2017) Pornpimol Charoentong et al.   Cell Reports

Sentinel Lymph Node Genes to Predict Prognosis in Node-Positive Melanoma Patients

(2016) Hongying Hao et al.   ANNALS OF SURGICAL ONCOLOGY

Conpair: concordance and contamination estimator for matched tumor–normal pairs

(2016) Ewa A. Bergmann et al.   BIOINFORMATICS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Facilitating T Cell Infiltration in Tumor Microenvironment Overcomes Resistance to PD-L1 Blockade

(2016) Haidong Tang et al.   CANCER CELL

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

(2016) Willy Hugo et al.   CELL

The Where, the When, and the How of Immune Monitoring for Cancer Immunotherapies in the Era of Checkpoint Inhibition

(2016) P. S. Hegde et al.   CLINICAL CANCER RESEARCH

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(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

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

The "cancer immunogram"

(2016) C. U. Blank et al.   SCIENCE

Repair of UVB-induced DNA damage is reduced in melanoma due to low XPC and global genome repair

(2016) Timothy Budden et al.   Oncotarget

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

(2016) Marios Giannakis et al.   Cell Reports

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade

(2016) Tavi Nathanson et al.   Cancer Immunology Research

Association of Biomarker-Based Treatment Strategies With Response Rates and Progression-Free Survival in Refractory Malignant Neoplasms

(2016) Maria Schwaederle et al.   JAMA Oncology

Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers

(2016) Mitesh J. Borad et al.   Scientific Reports

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

(2015) Michael S. Rooney et al.   CELL

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

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

(2015) Stefani Spranger et al.   NATURE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

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

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

Molecular stratification of metastatic melanoma using gene expression profiling : Prediction of survival outcome and benefit from molecular targeted therapy

(2015) Helena Cirenajwis et al.   Oncotarget

TGFβ1 secreted by cancer-associated fibroblasts induces epithelial-mesenchymal transition of bladder cancer cells through lncRNA-ZEB2NAT

(2015) Junlong Zhuang et al.   Scientific Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

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

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

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Determination of prognosis in metastatic melanoma through integration of clinico-pathologic, mutation, mRNA, microRNA, and protein information

(2014) Kaushala Jayawardana et al.   INTERNATIONAL JOURNAL OF CANCER

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Comprehensive molecular characterization of urothelial bladder carcinoma

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A promoter-level mammalian expression atlas

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

(2014) Roy S. Herbst et al.   NATURE

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

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

Transcriptional Silencing by Polycomb-Group Proteins

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

Oncology Meets Immunology: The Cancer-Immunity Cycle

(2013) Daniel S. Chen et al.   IMMUNITY

Predictive Gene Signature in MAGE-A3 Antigen-Specific Cancer Immunotherapy

(2013) Fernando Ulloa-Montoya et al.   JOURNAL OF CLINICAL ONCOLOGY

Transcriptome Profiling Identifies HMGA2 as a Biomarker of Melanoma Progression and Prognosis

(2013) Leon Raskin et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

A Molecular Taxonomy for Urothelial Carcinoma

(2012) G. Sjodahl et al.   CLINICAL CANCER RESEARCH

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

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

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

BioGPS and MyGene.info: organizing online, gene-centric information

(2012) Chunlei Wu et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Gene Expression Profiling-Based Identification of Molecular Subtypes in Stage IV Melanomas with Different Clinical Outcome

(2010) G. Jonsson et al.   CLINICAL CANCER RESEARCH

Gene Expression Signatures as a Guide to Treatment Strategies for In-Transit Metastatic Melanoma

(2010) Christina K. Augustine et al.   MOLECULAR CANCER THERAPEUTICS

ENCODE whole-genome data in the UCSC genome browser (2011 update)

(2010) Brian J. Raney et al.   NUCLEIC ACIDS RESEARCH

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(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival

(2009) D. Bogunovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Gene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases

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