A biobank of patient-derived pediatric brain tumor models

[1]  David T. W. Jones,et al.  Molecular heterogeneity and CXorf67 alterations in posterior fossa group A (PFA) ependymomas , 2018, Acta Neuropathologica.

[2]  David T. W. Jones,et al.  DNA methylation-based classification of central nervous system tumours , 2018, Nature.

[3]  Harry W. Clifford,et al.  Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts , 2018, BMC Genomics.

[4]  Kun Mu,et al.  Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma , 2017, Cancer cell.

[5]  Anang A. Shelat,et al.  Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors , 2017, Nature.

[6]  Roland Eils,et al.  The whole-genome landscape of medulloblastoma subtypes , 2017, Nature.

[7]  Melissa J. Davis,et al.  Inhibition of CDK4/6 by Palbociclib Significantly Extends Survival in Medulloblastoma Patient-Derived Xenograft Mouse Models , 2017, Clinical Cancer Research.

[8]  David T. W. Jones,et al.  H3-/IDH-wild type pediatric glioblastoma is comprised of molecularly and prognostically distinct subtypes with associated oncogenic drivers , 2017, Acta Neuropathologica.

[9]  K. Aldape,et al.  The current consensus on the clinical management of intracranial ependymoma and its distinct molecular variants , 2016, Acta Neuropathologica.

[10]  John W. Cassidy,et al.  A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds , 2016, Cell.

[11]  Donna Neuberg,et al.  The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. , 2016, Cancer cell.

[12]  Mei Lu,et al.  Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. , 2016, Cancer cell.

[13]  G. Reifenberger,et al.  The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary , 2016, Acta Neuropathologica.

[14]  Donna Neuberg,et al.  The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. , 2016, Cancer cell.

[15]  Roland Eils,et al.  Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes. , 2016, Cancer cell.

[16]  J. Olson,et al.  HDAC and PI3K Antagonists Cooperate to Inhibit Growth of MYC-Driven Medulloblastoma. , 2016, Cancer cell.

[17]  Wassim Raffoul,et al.  A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response. , 2016, Cancer cell.

[18]  Roland Eils,et al.  New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs , 2016, Cell.

[19]  X. Wang,et al.  Medulloblastoma subgroup-specific outcomes in irradiated children: who are the true high-risk patients? , 2016, Neuro-oncology.

[20]  Joshua M. Korn,et al.  High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response , 2015, Nature Medicine.

[21]  Chibo Hong,et al.  DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors. , 2015, Cancer cell.

[22]  Laura M. Heiser,et al.  Tumor-Derived Cell Lines as Molecular Models of Cancer Pharmacogenomics , 2015, Molecular Cancer Research.

[23]  Ranadip Pal,et al.  Erratum: Functionally defined therapeutic targets in diffuse intrinsic pontine glioma , 2015, Nature Medicine.

[24]  Nicholas J. Wang,et al.  Functionally-defined Therapeutic Targets in Diffuse Intrinsic Pontine Glioma , 2015, Nature Medicine.

[25]  Gary D Bader,et al.  Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups. , 2015, Cancer cell.

[26]  Florence I. Raynaud,et al.  Combined MYC and P53 Defects Emerge at Medulloblastoma Relapse and Define Rapidly Progressive, Therapeutically Targetable Disease , 2015, Cancer cell.

[27]  T. MacDonald,et al.  A Five-Gene Hedgehog Signature Developed as a Patient Preselection Tool for Hedgehog Inhibitor Therapy in Medulloblastoma , 2014, Clinical Cancer Research.

[28]  Sohrab P. Shah,et al.  Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution , 2014, Nature.

[29]  S. Pfister,et al.  Molecular Insights into Pediatric Brain Tumors Have the Potential to Transform Therapy , 2014, Clinical Cancer Research.

[30]  Gary D Bader,et al.  Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma , 2014, Nature.

[31]  Andrew J. Oler,et al.  Endogenous retrovirus induces leukemia in a xenograft mouse model for primary myelofibrosis , 2014, Proceedings of the National Academy of Sciences.

[32]  David T. W. Jones,et al.  Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing , 2014, Nature.

[33]  Susan M. Chang,et al.  Phase I/II study of erlotinib and temsirolimus for patients with recurrent malignant gliomas: North American Brain Tumor Consortium trial 04-02. , 2014, Neuro-oncology.

[34]  Toshihiro Kumabe,et al.  Cytogenetic prognostication within medulloblastoma subgroups. , 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[35]  Li Ding,et al.  C11orf95-RELA fusions drive oncogenic NF-κB signaling in ependymoma , 2014, Nature.

[36]  Manuel Hidalgo,et al.  Patient-derived xenograft models: an emerging platform for translational cancer research. , 2014, Cancer discovery.

[37]  J. Olson,et al.  Sonic Hedgehog-Induced Histone Deacetylase Activation Is Required for Cerebellar Granule Precursor Hyperplasia in Medulloblastoma , 2013, PloS one.

[38]  Volker Hovestadt,et al.  Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays , 2013, Acta Neuropathologica.

[39]  Timothy E. Reddy,et al.  Dynamic DNA methylation across diverse human cell lines and tissues , 2013, Genome research.

[40]  David T. W. Jones,et al.  Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. , 2012, Cancer cell.

[41]  Zhongming Zhao,et al.  TSGene: a web resource for tumor suppressor genes , 2012, Nucleic Acids Res..

[42]  Horatiu Voicu,et al.  Global gene expression profiling confirms the molecular fidelity of primary tumor-based orthotopic xenograft mouse models of medulloblastoma. , 2012, Neuro-oncology.

[43]  Scott L. Pomeroy,et al.  Molecular subgroups of medulloblastoma: the current consensus , 2011, Acta Neuropathologica.

[44]  Gary D Bader,et al.  Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. , 2011, Cancer cell.

[45]  Süleyman Cenk Sahinalp,et al.  deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data , 2011, PLoS Comput. Biol..

[46]  John T. E. Richardson The analysis of 2 × 2 contingency tables—Yet again , 2011, Statistics in medicine.

[47]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[48]  Amar Gajjar,et al.  Cross-species genomics matches driver mutations and cell compartments to model ependymoma , 2010, Nature.

[49]  S. Toms,et al.  Phase II trial of erlotinib with temozolomide and radiation in patients with newly diagnosed glioblastoma multiforme , 2010, Journal of Neuro-Oncology.

[50]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[51]  J. Olson,et al.  Response of preclinical medulloblastoma models to combination therapy with 13-cis retinoic acid and suberoylanilide hydroxamic acid (SAHA) , 2008, Journal of Neuro-Oncology.

[52]  Joseph Zeidner,et al.  The pediatric preclinical testing program: Description of models and early testing results , 2007, Pediatric blood & cancer.

[53]  I. Campbell Chi‐squared and Fisher–Irwin tests of two‐by‐two tables with small sample recommendations , 2007, Statistics in medicine.

[54]  B. Scheithauer,et al.  The 2007 WHO Classification of Tumours of the Central Nervous System , 2007, Acta Neuropathologica.

[55]  P. Burger,et al.  Phase III study of craniospinal radiation therapy followed by adjuvant chemotherapy for newly diagnosed average-risk medulloblastoma. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[56]  Yuri Kotliarov,et al.  Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines. , 2006, Cancer cell.

[57]  J. Biegel Molecular genetics of atypical teratoid/rhabdoid tumors , 2006 .

[58]  R. Gilbertson Brain Tumors Provide New Clues to the Source of Cancer Stem Cells: Does Oncology Recapitulate Ontogeny? , 2006, Cell cycle.

[59]  Crispin J. Miller,et al.  Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis , 2005, Bioinform..

[60]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[61]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[62]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[63]  D. Goldenberg,et al.  In vivo horizontal oncogenesis by a human tumor in nude mice. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[64]  K. Aldape,et al.  A phase II study of bevacizumab and erlotinib after radiation and temozolomide in MGMT unmethylated GBM patients , 2015, Journal of Neuro-Oncology.

[65]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[66]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[67]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[68]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .

[69]  J. Biegel Molecular genetics of atypical teratoid/rhabdoid tumor. , 2006, Neurosurgical focus.