Whole Genome Sequencing-Based Discovery of Structural Variants in Glioblastoma.

[1]  Neville E. Sanjana,et al.  CRISPR Screens to Discover Functional Noncoding Elements. , 2016, Trends in genetics : TIG.

[2]  V. Jobanputra,et al.  Abstract 4497: NYGC glioblastoma clinical outcomes pilot study: Discovering therapeutic potential in glioblastoma through integrative genomics , 2016 .

[3]  Vladimir Vacic,et al.  Conpair: concordance and contamination estimator for matched tumor–normal pairs , 2016, Bioinform..

[4]  C. Baker,et al.  Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. , 2016, American journal of human genetics.

[5]  Shawn M. Gillespie,et al.  Insulator dysfunction and oncogene activation in IDH mutant gliomas , 2015, Nature.

[6]  M. Gilbert,et al.  Advances in the treatment of newly diagnosed glioblastoma , 2015, BMC Medicine.

[7]  Donavan T. Cheng,et al.  Precision medicine at Memorial Sloan Kettering Cancer Center: clinical next-generation sequencing enabling next-generation targeted therapy trials. , 2015, Drug discovery today.

[8]  Euiseok J. Kim,et al.  Adult Lineage-Restricted CNS Progenitors Specify Distinct Glioblastoma Subtypes. , 2015, Cancer cell.

[9]  D. Reardon,et al.  Afatinib, an irreversible ErbB family blocker, with protracted temozolomide in recurrent glioblastoma: A case report , 2015, Oncotarget.

[10]  Ole Schulz-Trieglaff,et al.  Manta: Rapid detection of structural variants and indels for clinical sequencing applications , 2015, bioRxiv.

[11]  Timothy C Ryken,et al.  Toward precision medicine in glioblastoma: the promise and the challenges. , 2015, Neuro-oncology.

[12]  Obi L. Griffith,et al.  Optimizing cancer genome sequencing and analysis. , 2015, Cell systems.

[13]  Joshua M. Stuart,et al.  Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection , 2015, Nature Methods.

[14]  Donavan T. Cheng,et al.  Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. , 2015, The Journal of molecular diagnostics : JMD.

[15]  T. Cloughesy,et al.  Heterogeneity of epidermal growth factor receptor signalling networks in glioblastoma , 2015, Nature Reviews Cancer.

[16]  Joon-Oh Park,et al.  Constitutive asymmetric dimerization drives oncogenic activation of epidermal growth factor receptor carboxyl-terminal deletion mutants , 2015, Oncotarget.

[17]  Nicolai J. Birkbak,et al.  Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome , 2015, Annals of oncology : official journal of the European Society for Medical Oncology.

[18]  Na Li,et al.  Rational development and characterization of humanized anti–EGFR variant III chimeric antigen receptor T cells for glioblastoma , 2015, Science Translational Medicine.

[19]  H. Ellis,et al.  Current Therapeutic Advances Targeting EGFR and EGFRvIII in Glioblastoma , 2015, Front. Oncol..

[20]  Lei Shang,et al.  Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants , 2014, Proceedings of the National Academy of Sciences.

[21]  S. Antonarakis,et al.  Extrachromosomal driver mutations in glioblastoma and low grade glioma , 2014, Nature Communications.

[22]  Sohrab P. Shah,et al.  TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data , 2014, Genome research.

[23]  Benjamin M. Good,et al.  Organizing knowledge to enable personalization of medicine in cancer , 2014, Genome Biology.

[24]  Franziska Michor,et al.  Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma. , 2014, Cancer cell.

[25]  Shawn M. Gillespie,et al.  Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma , 2014, Science.

[26]  Steven J. M. Jones,et al.  Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma , 2014, Science.

[27]  S. Nelson,et al.  Targeted Therapy Resistance Mediated by Dynamic Regulation of Extrachromosomal Mutant EGFR DNA , 2014, Science.

[28]  Savita Shrivastava,et al.  Validation of a next-generation sequencing assay for clinical molecular oncology. , 2014, The Journal of molecular diagnostics : JMD.

[29]  L. Deangelis,et al.  Glioblastoma and other malignant gliomas: a clinical review. , 2013, JAMA.

[30]  H. Gan,et al.  The epidermal growth factor receptor variant III (EGFRvIII): where wild things are altered , 2013, The FEBS journal.

[31]  Benjamin J. Raphael,et al.  Mutational landscape and significance across 12 major cancer types , 2013, Nature.

[32]  K. Aldape,et al.  EGFR and EGFRvIII in glioblastoma: partners in crime. , 2013, Cancer cell.

[33]  D. Haussler,et al.  The Somatic Genomic Landscape of Glioblastoma , 2013, Cell.

[34]  S. Gabriel,et al.  Pan-cancer patterns of somatic copy-number alteration , 2013, Nature Genetics.

[35]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[36]  Trevor J Pugh,et al.  Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation , 2013, Nucleic acids research.

[37]  A. Wilm,et al.  LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets , 2012, Nucleic acids research.

[38]  Thomas Zichner,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[39]  Wendy S. W. Wong,et al.  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs , 2012, Bioinform..

[40]  A. McKenna,et al.  Absolute quantification of somatic DNA alterations in human cancer , 2012, Nature Biotechnology.

[41]  Martin Vingron,et al.  Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS , 2012, Bioinform..

[42]  Mark D. Johnson,et al.  Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion , 2011, Proceedings of the National Academy of Sciences.

[43]  Michael C. Rusch,et al.  CREST maps somatic structural variation in cancer genomes with base-pair resolution , 2011, Nature Methods.

[44]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[45]  C. Perou,et al.  Allele-specific copy number analysis of tumors , 2010, Proceedings of the National Academy of Sciences.

[46]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[47]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[48]  R. Wilson,et al.  BreakDancer: An algorithm for high resolution mapping of genomic structural variation , 2009, Nature Methods.

[49]  Kai Ye,et al.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..

[50]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[51]  Joshua M. Korn,et al.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2008, Nature.

[52]  S. Gabriel,et al.  Epidermal Growth Factor Receptor Activation in Glioblastoma through Novel Missense Mutations in the Extracellular Domain , 2006, PLoS medicine.

[53]  Tracy T Batchelor,et al.  A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy. , 2006, Cancer research.

[54]  C. James,et al.  Identical splicing of aberrant epidermal growth factor receptor transcripts from amplified rearranged genes in human glioblastomas. , 1990, Proceedings of the National Academy of Sciences of the United States of America.