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

Cancer Cell - Tập 17 Số 1 - Trang 98-110 - 2010
Roel G.W. Verhaak1,2, Katherine A. Hoadley3,4, Elizabeth Purdom5, Victoria Wang6, Yuan Qi7,4, Matthew D. Wilkerson7,4, C. Ryan Miller8,4, Li Ding9, Todd R. Golub10,2, Jill P. Mesirov2, Gabriele Alexe2, Michael S. Lawrence1,2, Michael O'Kelly1,2, Pablo Tamayo2, Barbara A. Weir1,2, Stacey Gabriel2, Wendy Winckler1,2, Supriya Gupta2, Lakshmi R. Jakkula11, Heidi S. Feiler11, John Hodgson12, C. David James12, Jann N. Sarkaria13, Cameron Brennan14, A Kahn15, Paul T. Spellman11, Richard K. Wilson9, Terence P. Speed5,16, Joe W. Gray11, Matthew Meyerson1,2, Gad Getz2, Charles M. Perou3,6,4, D. Neil Hayes7,4
1Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA
2The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
3Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
4Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
5Department of Statistics, University of California, Berkeley, CA 94720, USA
6Group in Biostatistics, University of California, Berkeley, CA 94720, USA
7Department of Internal Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
8Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
9The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
10Department of Pediatric Oncology, Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA
11Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
12Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
13Department of Radiation Oncology, Mayo Clinic, Rochester, MN 55905, USA
14Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
15SRA International, Fairfax, VA 22033, USA
16Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia

Tóm tắt

Từ khóa


Tài liệu tham khảo

Arjona, 2006, Early genetic changes involved in low-grade astrocytic tumor development, Curr. Mol. Med., 6, 645, 10.2174/156652406778195017

Barbie, 2009, Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1, Nature, 462, 108, 10.1038/nature08460

Beroukhim, 2007, Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma, Proc. Natl. Acad. Sci. USA, 104, 20007, 10.1073/pnas.0710052104

Brennan, 2009, Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations, PLoS ONE, 4, e7752, 10.1371/journal.pone.0007752

Cahoy, 2008, A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function, J. Neurosci., 28, 264, 10.1523/JNEUROSCI.4178-07.2008

Curran, 1993, Recursive partitioning analysis of prognostic factors in three Radiation Therapy Oncology Group malignant glioma trials, J. Natl. Cancer Inst., 85, 704, 10.1093/jnci/85.9.704

Dabney, 2006, ClaNC: point-and-click software for classifying microarrays to nearest centroids, Bioinformatics, 22, 122, 10.1093/bioinformatics/bti756

Dennis, 2003, DAVID: Database for Annotation, Visualization, and Integrated Discovery, Genome Biol., 4, P3, 10.1186/gb-2003-4-5-p3

Freije, 2004, Gene expression profiling of gliomas strongly predicts survival, Cancer Res., 64, 6503, 10.1158/0008-5472.CAN-04-0452

Furnari, 2007, Malignant astrocytic glioma: genetics, biology, and paths to treatment, Genes Dev., 21, 2683, 10.1101/gad.1596707

Galli, 2004, Isolation and characterization of tumorigenic, stem-like neural precursors from human glioblastoma, Cancer Res., 64, 7011, 10.1158/0008-5472.CAN-04-1364

Hegi, 2005, MGMT gene silencing and benefit from temozolomide in glioblastoma, N. Engl. J. Med., 352, 997, 10.1056/NEJMoa043331

Hodgson, 2009, Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts, Neuro. Oncol., 11, 477, 10.1215/15228517-2008-113

Huber, 2004, Matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements, Bioinformatics, 20, 1651, 10.1093/bioinformatics/bth133

Hunter, 2006, A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy, Cancer Res., 66, 3987, 10.1158/0008-5472.CAN-06-0127

Irizarry, 2003, Summaries of Affymetrix GeneChip probe level data, Nucleic Acids Res., 31, e15, 10.1093/nar/gng015

Jackson, 2006, PDGFR alpha-positive B cells are neural stem cells in the adult SVZ that form glioma-like growths in response to increased PDGF signaling, Neuron, 51, 187, 10.1016/j.neuron.2006.06.012

Kleihues, 1999, Primary and secondary glioblastomas: from concept to clinical diagnosis, Neuro-oncol., 1, 44, 10.1093/neuonc/1.1.44

Kreth, 1999, The role of tumor resection in the treatment of glioblastoma multiforme in adults, Cancer, 86, 2117, 10.1002/(SICI)1097-0142(19991115)86:10<2117::AID-CNCR33>3.0.CO;2-8

Kumabe, 1992, Amplification of alpha-platelet-derived growth factor receptor gene lacking an exon coding for a portion of the extracellular region in a primary brain tumor of glial origin, Oncogene, 7, 627

Liang, 2005, Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme, Proc. Natl. Acad. Sci. USA, 102, 5814, 10.1073/pnas.0402870102

Ligon, 2007, Olig2-regulated lineage-restricted pathway controls replication competence in neural stem cells and malignant glioma, Neuron, 53, 503, 10.1016/j.neuron.2007.01.009

Liu, 2007, AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets, Bioinformatics, 23, 2385, 10.1093/bioinformatics/btm360

Liu, 2008, Statistical significance of clustering for high dimension low sample size data, J. Am. Stat. Assoc., 103, 1281, 10.1198/016214508000000454

Mardia, 1979

Mischel, 2003, Identification of molecular subtypes of glioblastoma by gene expression profiling, Oncogene, 22, 2361, 10.1038/sj.onc.1206344

Monti, 2003, Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data, Mach. Learn., 52, 91, 10.1023/A:1023949509487

Murat, 2008, Stem cell-related “self-renewal” signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma, J. Clin. Oncol., 26, 3015, 10.1200/JCO.2007.15.7164

Noble, 2004, Getting a GR(i)P on oligodendrocyte development, Dev. Biol., 265, 33, 10.1016/j.ydbio.2003.06.002

Nutt, 2003, Gene expression-based classification of malignant gliomas correlates better with survival than histological classification, Cancer Res., 63, 1602

Ohgaki, 2005, Epidemiology and etiology of gliomas, Acta Neuropathol., 109, 93, 10.1007/s00401-005-0991-y

Olshen, 2004, Circular binary segmentation for the analysis of array-based DNA copy number data, Biostatistics, 5, 557, 10.1093/biostatistics/kxh008

Phillips, 2006, Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis, Cancer Cell, 9, 157, 10.1016/j.ccr.2006.02.019

2008

Rand, 2005, Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas, Proc. Natl. Acad. Sci. USA, 102, 14344, 10.1073/pnas.0507200102

Rousseeuw, 1987, Silhouettes: A graphical aid to the interpretation and validation of cluster analysis, J. Comput. Appl. Math., 20, 53, 10.1016/0377-0427(87)90125-7

Ruano, 2006, Identification of novel candidate target genes in amplicons of glioblastoma multiforme tumors detected by expression and CGH microarray profiling, Mol. Cancer, 5, 39, 10.1186/1476-4598-5-39

Sanai, 2005, Neural stem cells and the origin of gliomas, N. Engl. J. Med., 353, 811, 10.1056/NEJMra043666

Scott, 1998, Validation and predictive power of Radiation Therapy Oncology Group (RTOG) recursive partitioning analysis classes for malignant glioma patients: a report using RTOG 90-06, Int. J. Radiat. Oncol. Biol. Phys., 40, 51, 10.1016/S0360-3016(97)00485-9

Shai, 2003, Gene expression profiling identifies molecular subtypes of gliomas, Oncogene, 22, 4918, 10.1038/sj.onc.1206753

Sun, 2006, Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain, Cancer Cell, 9, 287, 10.1016/j.ccr.2006.03.003

2008, Comprehensive genomic characterization defines human glioblastoma genes and core pathways, Nature, 455, 1061, 10.1038/nature07385

Thiery, 2002, Epithelial-mesenchymal transitions in tumour progression, Nat. Rev. Cancer, 2, 442, 10.1038/nrc822

Tso, 2006, Distinct transcription profiles of primary and secondary glioblastoma subgroups, Cancer Res., 66, 159, 10.1158/0008-5472.CAN-05-0077

Tusher, 2001, Significance analysis of microarrays applied to the ionizing radiation response, Proc. Natl. Acad. Sci. USA, 98, 5116, 10.1073/pnas.091062498

Watanabe, 1996, Overexpression of the EGF receptor and p53 mutations are mutually exclusive in the evolution of primary and secondary glioblastomas, Brain Pathol., 6, 217, 10.1111/j.1750-3639.1996.tb00848.x

Whitfield, 2002, Identification of genes periodically expressed in the human cell cycle and their expression in tumors, Mol. Biol. Cell, 13, 1977, 10.1091/mbc.02-02-0030.

Yan, 2009, IDH1 and IDH2 mutations in gliomas, N. Engl. J. Med., 360, 765, 10.1056/NEJMoa0808710

Zhu, 2002, Neurofibromas in NF1: Schwann cell origin and role of tumor environment, Science, 296, 920, 10.1126/science.1068452

Thông tin
Thông tin xuất bản

Cancer Cell

Tập 17 Số 1

98-110

Thông tin tác giả