Immunogenomic analysis of human brain metastases reveals diverse immune landscapes across genetically distinct tumors

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

(2022) Bastien Nguyen et al.   CELL

Cellular architecture of human brain metastases

(2022) Hugo Gonzalez et al.   CELL

Changing characteristics, treatment approaches and survival of patients with brain metastasis: data from six thousand and thirty-one individuals over an observation period of 30 years

(2022) Ariane Steindl et al.   EUROPEAN JOURNAL OF CANCER

Mapping molecular subtype specific alterations in breast cancer brain metastases identifies clinically relevant vulnerabilities

(2022) Nicola Cosgrove et al.   Nature Communications

Hallmarks of Cancer: New Dimensions

(2022) Douglas Hanahan   Cancer Discovery

Tumor Immune Microenvironment of Brain Metastases: Toward Unlocking Antitumor Immunity

(2022) Matthew R. Strickland et al.   Cancer Discovery

Multi-omic molecular profiling reveals potentially targetable abnormalities shared across multiple histologies of brain metastasis

(2021) Kazutaka Fukumura et al.   ACTA NEUROPATHOLOGICA

A MyD88/IL-1R axis regulates PD-1 expression on tumor-associated macrophages and sustains their immunosuppressive function in melanoma

(2021) Sarang Tartey et al.   CANCER RESEARCH

The origins and genetic interactions of KRAS mutations are allele- and tissue-specific

(2021) Joshua H. Cook et al.   Nature Communications

Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

(2021) Alexander Bagaev et al.   CANCER CELL

In silico saturation mutagenesis of cancer genes

(2021) Ferran Muiños et al.   NATURE

BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells

(2021) Hyungseok Seo et al.   NATURE IMMUNOLOGY

BATF regulates progenitor to cytolytic effector CD8+ T cell transition during chronic viral infection

(2021) Yao Chen et al.   NATURE IMMUNOLOGY

An integrated pipeline for comprehensive analysis of immune cells in human brain tumor clinical samples

(2021) Roeltje R. Maas et al.   Nature Protocols

Interpretation of T cell states from single-cell transcriptomics data using reference atlases

(2021) Massimo Andreatta et al.   Nature Communications

Genomic and transcriptomic analyses of breast cancer primaries and matched metastases in AURORA, the Breast International Group (BIG) molecular screening initiative

(2021) Philippe Aftimos et al.   Cancer Discovery

Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification

(2021) Andrew M. Leader et al.   CANCER CELL

Mutational profiles of primary pulmonary adenocarcinoma and paired brain metastases disclose the importance of KRAS mutations

(2021) Erik Vassella et al.   EUROPEAN JOURNAL OF CANCER

Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis

(2021) Maximilian O. Schaettler et al.   Cancer Discovery

Current approaches to the management of brain metastases

(2020) John H. Suh et al.   Nature Reviews Clinical Oncology

pVACtools: a computational toolkit to identify and visualize cancer neoantigens

(2020) Jasreet Hundal et al.   Cancer Immunology Research

Single-Cell Mapping of Human Brain Cancer Reveals Tumor-Specific Instruction of Tissue-Invading Leukocytes

(2020) Ekaterina Friebel et al.   CELL

Interrogation of the Microenvironmental Landscape in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells

(2020) Florian Klemm et al.   CELL

Pembrolizumab for management of patients with NSCLC and brain metastases: long-term results and biomarker analysis from a non-randomised, open-label, phase 2 trial

(2020) Sarah B Goldberg et al.   LANCET ONCOLOGY

Genomic characterization of human brain metastases identifies drivers of metastatic lung adenocarcinoma

(2020) David J. H. Shih et al.   NATURE GENETICS

TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy

(2020) Martina Molgora et al.   CELL

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

(2020) Francesca Petralia et al.   CELL

A Blazing Landscape: Neuroinflammation Shapes Brain Metastasis

(2019) Hila Doron et al.   CANCER RESEARCH

Efficacy and safety of the combination of nivolumab (NIVO) plus ipilimumab (IPI) in patients with symptomatic melanoma brain metastases (CheckMate 204).

(2019) Hussein Abdul-Hassan Tawbi et al.   JOURNAL OF CLINICAL ONCOLOGY

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer

(2019) Leticia De Mattos-Arruda et al.   Cell Reports

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers

(2019) Claudia Arnedo-Pac et al.   BIOINFORMATICS

Loss of p53 triggers WNT-dependent systemic inflammation to drive breast cancer metastasis

(2019) Max D. Wellenstein et al.   NATURE

Self-maintaining CD103+ cancer-specific T cells are highly energetic with rapid cytotoxic and effector responses

(2019) Megat Abd Hamid et al.   Cancer Immunology Research

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Diverse genetic-driven immune landscapes dictate tumor progression through distinct mechanisms

(2018) Marco Bezzi et al.   NATURE MEDICINE

Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures

(2018) Jongkeun Lee et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Thomas Duhen et al.   Nature Communications

S100 Proteins As an Important Regulator of Macrophage Inflammation

(2018) Chang Xia et al.   Frontiers in Immunology

Combined Nivolumab and Ipilimumab in Melanoma Metastatic to the Brain

(2018) Hussein A. Tawbi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evolution of Metastases in Space and Time under Immune Selection

(2018) Mihaela Angelova et al.   CELL

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

Tumour-elicited neutrophils engage mitochondrial metabolism to circumvent nutrient limitations and maintain immune suppression

(2018) Christopher M. Rice et al.   Nature Communications

Estimating Survival in Melanoma Patients With Brain Metastases: An Update of the Graded Prognostic Assessment for Melanoma Using Molecular Markers (Melanoma-molGPA)

(2017) Paul W. Sperduto et al.   INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS

Integrative clinical genomics of metastatic cancer

(2017) Dan R. Robinson et al.   NATURE

Estimating Survival in Patients With Lung Cancer and Brain Metastases

(2017) Paul W. Sperduto et al.   JAMA Oncology

Gene expression markers of Tumor Infiltrating Leukocytes

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

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

GenVisR: Genomic Visualizations in R

(2016) Zachary L. Skidmore et al.   BIOINFORMATICS

Pembrolizumab for patients with melanoma or non-small-cell lung cancer and untreated brain metastases: early analysis of a non-randomised, open-label, phase 2 trial

(2016) Sarah B Goldberg et al.   LANCET ONCOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Mutational signatures associated with tobacco smoking in human cancer

(2016) L. B. Alexandrov et al.   SCIENCE

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels

(2016) Matteo D’Antonio et al.   Cell Reports

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

(2016) Eric Talevich et al.   PLoS Computational Biology

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations

(2015) J. C. Hunter et al.   MOLECULAR CANCER RESEARCH

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

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

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

(2015) N. A. Rizvi et al.   SCIENCE

Cerebrospinal fluid-derived circulating tumour DNA better represents the genomic alterations of brain tumours than plasma

(2015) Leticia De Mattos-Arruda et al.   Nature Communications

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

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

CopywriteR: DNA copy number detection from off-target sequence data

(2015) Thomas Kuilman et al.   GENOME BIOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

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

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

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

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis

(2013) Benjamin JM Taylor et al.   eLife

Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing

(2012) Pengyuan Liu et al.   CARCINOGENESIS

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

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

(2010) Heng Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH