Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology

Revealing and Harnessing Tumour-Associated Microglia/Macrophage Heterogeneity in Glioblastoma

(2020) Yolanda Pires-Afonso et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis

(2020) Yvonne A. Evrard et al.   CANCER RESEARCH

Challenges to curing primary brain tumours

(2019) Kenneth Aldape et al.   Nature Reviews Clinical Oncology

Evolutionary Trajectories of IDHWT Glioblastomas Reveal a Common Path of Early Tumorigenesis Instigated Years ahead of Initial Diagnosis

(2019) Verena Körber et al.   CANCER CELL

Drug Efficacy Comparison of 3D Forming and Preforming Sphere Models with a Micropillar and Microwell Chip Platform

(2019) Il Doh et al.   SLAS Discovery

Molecular Pathology of Tumors of the Central Nervous System

(2019) B W Kristensen et al.   ANNALS OF ONCOLOGY

Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis

(2019) Qinjie Weng et al.   Cell Stem Cell

PI3K/AKT/mTOR Pathway Alterations Promote Malignant Progression and Xenograft Formation in Oligodendroglial Tumors

(2019) Kensuke Tateishi et al.   CLINICAL CANCER RESEARCH

Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment

(2019) Anne Dirkse et al.   Nature Communications

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients

(2019) Petr V. Nazarov et al.   BMC Medical Genomics

Patient-derived xenografts of central nervous system metastasis reveal expansion of aggressive minor clones

(2019) Ben Yi Tew et al.   NEURO-ONCOLOGY

Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments

(2019) Yaoqing Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Evolution of IDH Wild-Type Glioblastomas Treated With Standard of Care Affects Survival and Design of Precision Medicine Trials: A Report From the EORTC 1542 Study

(2019) Kaspar Draaisma et al.   JOURNAL OF CLINICAL ONCOLOGY

Longitudinal molecular trajectories of diffuse glioma in adults

(2019) Floris P. Barthel et al.   NATURE

IDH mutant lower grade (WHO Grades II/III) astrocytomas can be stratified for risk by CDKN2A, CDK4 and PDGFRA copy number alterations

(2019) Rui Ryan Yang et al.   BRAIN PATHOLOGY

A Patient-Derived Glioblastoma Organoid Model and Biobank Recapitulates Inter- and Intra-tumoral Heterogeneity

(2019) Fadi Jacob et al.   CELL

Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma

(2019) Rachael A. Vaubel et al.   CLINICAL CANCER RESEARCH

Novel, improved grading system(s) for IDH-mutant astrocytic gliomas

(2018) Mitsuaki Shirahata et al.   ACTA NEUROPATHOLOGICA

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts

(2018) Maurizio Callari et al.   BMC GENOMICS

Epidermal Growth Factor Receptor Extracellular Domain Mutations in Glioblastoma Present Opportunities for Clinical Imaging and Therapeutic Development

(2018) Zev A. Binder et al.   CANCER CELL

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

DNA methylation-based classification of central nervous system tumours

(2018) David Capper et al.   NATURE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma

(2018) Ana C. deCarvalho et al.   NATURE GENETICS

Primary glioblastoma cells for precision medicine: a quantitative portrait of genomic (in)stability during the first 30 passages

(2018) Sathishkumar Baskaran et al.   NEURO-ONCOLOGY

Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium

(2018) et al.   NEURO-ONCOLOGY

A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence

(2018) Camila Ferreira de Souza et al.   Cell Reports

Using PDX for Preclinical Cancer Drug Discovery: The Evolving Field

(2018) Juliet Williams   Journal of Clinical Medicine

Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy

(2018) Jin-Ku Lee et al.   NATURE GENETICS

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

(2018) Johanna Klughammer et al.   NATURE MEDICINE

A biobank of patient-derived pediatric brain tumor models

(2018) Sebastian Brabetz et al.   NATURE MEDICINE

PDX Finder: A portal for patient-derived tumor xenograft model discovery

(2018) Nathalie Conte et al.   NUCLEIC ACIDS RESEARCH

Dianhydrogalactitol induces replication-dependent DNA damage in tumor cells preferentially resolved by homologous recombination

(2018) Beibei Zhai et al.   Cell Death & Disease

Lack of functional normalisation of tumour vessels following anti-angiogenic therapy in glioblastoma

(2017) Nina Obad et al.   JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM

Patient-derived xenografts undergo mouse-specific tumor evolution

(2017) Uri Ben-David et al.   NATURE GENETICS

EGFR heterogeneity and implications for therapeutic intervention in glioblastoma

(2017) Eskil Eskilsson et al.   NEURO-ONCOLOGY

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary

(2016) David N. Louis et al.   ACTA NEUROPATHOLOGICA

A Three-Dimensional Organoid Culture System Derived from Human Glioblastomas Recapitulates the Hypoxic Gradients and Cancer Stem Cell Heterogeneity of Tumors Found In Vivo

(2016) Christopher G. Hubert et al.   CANCER RESEARCH

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

(2016) Michele Ceccarelli et al.   CELL

Clonal evolution of glioblastoma under therapy

(2016) Jiguang Wang et al.   NATURE GENETICS

Association between DNA Methylation in Whole Blood and Measures of Glucose Metabolism: KORA F4 Study

(2016) Jennifer Kriebel et al.   PLoS One

Molecular crosstalk between tumour and brain parenchyma instructs histopathological features in glioblastoma

(2016) Sébastien Bougnaud et al.   Oncotarget

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

(2016) Eric Talevich et al.   PLoS Computational Biology

Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets

(2015) Felix Sahm et al.   ACTA NEUROPATHOLOGICA

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

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

(2015) Hoon Kim et al.   GENOME RESEARCH

CDKN2ALoss Is Associated With Shortened Overall Survival in Lower-Grade (World Health Organization Grades II–III) Astrocytomas

(2015) Gerald F. Reis et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response

(2015) Hui Gao et al.   NATURE MEDICINE

Babelomics 5.0: functional interpretation for new generations of genomic data

(2015) Roberto Alonso et al.   NUCLEIC ACIDS RESEARCH

EGFRAmplification and Glioblastoma Stem-Like Cells

(2015) Katrin Liffers et al.   Stem Cells International

Targetable Signaling Pathway Mutations Are Associated with Malignant Phenotype in IDH-Mutant Gliomas

(2014) H. Wakimoto et al.   CLINICAL CANCER RESEARCH

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

(2014) Peter Eirew et al.   NATURE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

EGFR Variant Heterogeneity in Glioblastoma Resolved through Single-Nucleus Sequencing

(2014) J. M. Francis et al.   Cancer Discovery

U-251 revisited: genetic drift and phenotypic consequences of long-term cultures of glioblastoma cells

(2014) Anja Torsvik et al.   Cancer Medicine

EGFR wild-type amplification and activation promote invasion and development of glioblastoma independent of angiogenesis

(2013) Krishna M. Talasila et al.   ACTA NEUROPATHOLOGICA

Glioblastomas are composed of genetically divergent clones with distinct tumourigenic potential and variable stem cell-associated phenotypes

(2013) Daniel Stieber et al.   ACTA NEUROPATHOLOGICA

Side population in human glioblastoma is non-tumorigenic and characterizes brain endothelial cells

(2013) Anna Golebiewska et al.   BRAIN

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Spontaneous loss of heterozygosity leading to homozygous R132H in a patient-derived IDH1 mutant cell line

(2013) H. A. Luchman et al.   NEURO-ONCOLOGY

Serum-free culture success of glial tumors is related to specific molecular profiles and expression of extracellular matrix–associated gene modules

(2013) Rutger K. Balvers et al.   NEURO-ONCOLOGY

A Novel, Diffusely Infiltrative Xenograft Model of Human Anaplastic Oligodendroglioma with Mutations in FUBP1, CIC, and IDH1

(2013) Barbara Klink et al.   PLoS One

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics

(2013) A. Sottoriva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patient-Specific Orthotopic Glioblastoma Xenograft Models Recapitulate the Histopathology and Biology of Human Glioblastomas In Situ

(2013) Kyeung Min Joo et al.   Cell Reports

Increased mitochondrial activity in a novel IDH1-R132H mutant human oligodendroglioma xenograft model: in situ detection of 2-HG and α-KG

(2013) Anna C Navis et al.   Acta Neuropathologica Communications

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

(2012) Andrew E. Teschendorff et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Intratumoral heterogeneity of receptor tyrosine kinases EGFR and PDGFRA amplification in glioblastoma defines subpopulations with distinct growth factor response

(2012) N. J. Szerlip et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glioblastoma-Derived Epidermal Growth Factor Receptor Carboxyl-Terminal Deletion Mutants Are Transforming and Are Sensitive to EGFR-Directed Therapies

(2011) J. Cho et al.   CANCER RESEARCH

Heterogeneity Maintenance in Glioblastoma: A Social Network

(2011) R. Bonavia et al.   CANCER RESEARCH

Tumor invasion after treatment of glioblastoma with bevacizumab: radiographic and pathologic correlation in humans and mice

(2011) J. F. de Groot et al.   NEURO-ONCOLOGY

An in vivo patient-derived model of endogenous IDH1-mutant glioma

(2011) H. A. Luchman et al.   NEURO-ONCOLOGY

Maintenance of primary tumor phenotype and genotype in glioblastoma stem cells

(2011) H. Wakimoto et al.   NEURO-ONCOLOGY

Anti-VEGF treatment reduces blood supply and increases tumor cell invasion in glioblastoma

(2011) Olivier Keunen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A reproducible brain tumour model established from human glioblastoma biopsies

(2010) Jian Wang et al.   BMC CANCER

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

Differentiation Therapy Exerts Antitumor Effects on Stem-like Glioma Cells

(2010) B. Campos et al.   CLINICAL CANCER RESEARCH

Immunohistochemical Expression of Stem Cell, Endothelial Cell, and Chemosensitivity Markers in Primary Glioma Spheroids Cultured in Serum-Containing and Serum-Free Medium

(2010) Karina Christensen et al.   NEUROSURGERY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phenotypic and Genotypic Characterization of Orthotopic Human Glioma Models and Its Relevance for the Study of Anti-glioma Therapy

(2008) An Claes et al.   BRAIN PATHOLOGY

A novel eGFP-expressing immunodeficient mouse model to study tumor-host interactions

(2008) Simone P. Niclou et al.   FASEB JOURNAL