The Use of Global Profiling in Biomarker Development for Gliomas

The diffuse gliomas are a heterogeneous group of malignancies with highly variable outcomes and diagnosis is largely based on the histological appearance of the tumors. Tumor classification according to cello type and grade provides some prognostic information. However, the diversity of gliomas, within tumor type and grade categories, has made prognostic determinations based purely on clinicopathologic variables difficult. There is an increasing body of data suggesting a significant amount of molecular diversity accounts for the heterogeneity of clinical observations, such as response to treatment and time to progression. The last decade has witnessed an explosive advance in our knowledge of the molecular genetics of brain tumors, due in large part to the availability of high‐throughput profiling techniques, including new sequencing methodologies as well as multidimensional profiling by the Cancer Genome Atlas project. The large amount of data generated by these efforts has enabled the identification of prognostic and predictive factors and helping to identify pathways that are driving tumor growth. Identification of biomarkers, especially when coupled to clinical trials of newer targeted therapies, will enable better patient stratification and individualization of treatment.

[1]  R. Wilson,et al.  Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. , 2010, Cancer cell.

[2]  Howard Colman,et al.  MGMT promoter methylation is predictive of response to radiotherapy and prognostic in the absence of adjuvant alkylating chemotherapy for glioblastoma. , 2010, Neuro-oncology.

[3]  S. Gabriel,et al.  Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. , 2010, Cancer cell.

[4]  K. Aldape,et al.  A multigene predictor of outcome in glioblastoma. , 2010, Neuro-oncology.

[5]  Andrew P. Stubbs,et al.  Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. , 2009, Cancer research.

[6]  C. Brennan,et al.  Glioblastoma Subclasses Can Be Defined by Activity among Signal Transduction Pathways and Associated Genomic Alterations , 2009, PloS one.

[7]  Yuri Kotliarov,et al.  Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. , 2009, Cancer research.

[8]  F. Ducray,et al.  IDH1 and IDH2 mutations in gliomas. , 2009, The New England journal of medicine.

[9]  Calum MacAulay,et al.  SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes , 2008, BMC Bioinformatics.

[10]  D. Busam,et al.  An Integrated Genomic Analysis of Human Glioblastoma Multiforme , 2008, Science.

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

[12]  E. Mardis.  Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[13]  R. Britto,et al.  Novel Glioblastoma Markers with Diagnostic and Prognostic Value Identified through Transcriptome Analysis , 2008, Clinical Cancer Research.

[14]  Suely K. N. Marie,et al.  Gene expression profile analysis of primary glioblastomas and non-neoplastic brain tissue: identification of potential target genes by oligonucleotide microarray and real-time quantitative PCR , 2008, Journal of Neuro-Oncology.

[15]  Pedro Martínez,et al.  Identification of survival‐related genes of the phosphatidylinositol 3′‐kinase signaling pathway in glioblastoma multiforme , 2008, Cancer.

[16]  Candidate genes for the progression of malignant gliomas identified by microarray analysis , 2008, Neurosurgical Review.

[17]  E. Mardis.  The impact of next-generation sequencing technology on genetics. , 2008, Trends in genetics : TIG.

[18]  M. Nistér,et al.  Gene expression analyses of grade II gliomas and identification of rPTPβ/ζ as a candidate oligodendroglioma marker , 2008 .

[19]  M. Nistér,et al.  Gene expression analyses of grade II gliomas and identification of rPTPbeta/zeta as a candidate oligodendroglioma marker. , 2008, Neuro-oncology.

[20]  Jean-Yves Delattre,et al.  Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile , 2008, Molecular Cancer.

[21]  K. Baggerly,et al.  Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays , 2008, BMC Genomics.

[22]  K. Aldape,et al.  Aberrant FoxM1B expression increases matrix metalloproteinase-2 transcription and enhances the invasion of glioma cells , 2007, Oncogene.

[23]  Elisabet Englund,et al.  Microarray analysis of gliomas reveals chromosomal position-associated gene expression patterns and identifies potential immunotherapy targets , 2007, Journal of Neuro-Oncology.

[24]  M. J. van den Bent,et al.  Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. , 2007, Cancer research.

[25]  Charlie Teo,et al.  IQGAP1 and IGFBP2: Valuable Biomarkers for Determining Prognosis in Glioma Patients , 2007, Journal of neuropathology and experimental neurology.

[26]  J. Lafuente,et al.  Gene expression profiling of human gliomas reveals differences between GBM and LGA related to energy metabolism and notch signaling pathways , 2007, Journal of Molecular Neuroscience.

[27]  P. Liberski,et al.  Molecular profiling identifies prognostic subgroups of pediatric glioblastoma and shows increased YB-1 expression in tumors. , 2007, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[28]  J. Baker,et al.  Genomic Health, Inc. , 2007, Pharmacogenomics.

[29]  Leszek Paczek,et al.  Gene expression profile as a prognostic factor in high-grade gliomas. , 2007, International journal of oncology.

[30]  Fenghua Liu,et al.  A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma. , 2006, Cancer research.

[31]  A. Witteveen,et al.  Converting a breast cancer microarray signature into a high-throughput diagnostic test , 2006, BMC Genomics.

[32]  G. Reifenberger,et al.  Identification of novel oligodendroglioma‐associated candidate tumor suppressor genes in 1p36 and 19q13 using microarray‐based expression profiling , 2006, International journal of cancer.

[33]  Li Zhang,et al.  Prognostic Associations of Activated Mitogen-Activated Protein Kinase and Akt Pathways in Glioblastoma , 2006, Clinical Cancer Research.

[34]  Raymond Sawaya,et al.  FoxM1B is overexpressed in human glioblastomas and critically regulates the tumorigenicity of glioma cells. , 2006, Cancer research.

[35]  Thomas D. Wu,et al.  Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. , 2006, Cancer cell.

[36]  D. Allison,et al.  Microarray data analysis: from disarray to consolidation and consensus , 2006, Nature Reviews Genetics.

[37]  Jord H A Nagel,et al.  Gene expression profiles associated with treatment response in oligodendrogliomas. , 2005, Cancer research.

[38]  R. Britto,et al.  Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma , 2005, Oncogene.

[39]  Greg Yothers,et al.  Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. , 2005, The New England journal of medicine.

[40]  K. Aldape,et al.  YKL-40 Expression is Associated with Poorer Response to Radiation and Shorter Overall Survival in Glioblastoma , 2005, Clinical Cancer Research.

[41]  Kathleen F. Kerr,et al.  Standardizing global gene expression analysis between laboratories and across platforms , 2005, Nature Methods.

[42]  D. Botstein,et al.  Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Rebecca A Betensky,et al.  YKL-40 Is a Differential Diagnostic Marker for Histologic Subtypes of High-Grade Gliomas , 2005, Clinical Cancer Research.

[44]  R. Mirimanoff,et al.  MGMT gene silencing and benefit from temozolomide in glioblastoma. , 2005, The New England journal of medicine.

[45]  K. Aldape,et al.  Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma. , 2005, Cancer research.

[46]  M. Cronin,et al.  A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. , 2004, The New England journal of medicine.

[47]  F. Heppner,et al.  Gene expression profiling and subgroup identification of oligodendrogliomas , 2004, Oncogene.

[48]  Hiroyuki Aburatani,et al.  Selective Expression of a Subset of Neuronal Genes in Oligodendroglioma with Chromosome 1p Loss , 2004, Brain pathology.

[49]  K. Hess,et al.  Identification of Necrosis-Associated Genes in Glioblastoma by cDNA Microarray Analysis , 2004, Clinical Cancer Research.

[50]  Eytan Domany,et al.  Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. , 2003, Cancer research.

[51]  David E. Misek,et al.  Characterization of gene expression profiles associated with glioma progression using oligonucleotide-based microarray analysis and real-time reverse transcription-polymerase chain reaction. , 2003, The American journal of pathology.

[52]  Paul S Mischel,et al.  Gene expression profiling identifies molecular subtypes of gliomas , 2003, Oncogene.

[53]  D. Dressman,et al.  Overexpression of the EGFR/FKBP12/HIF-2alpha pathway identified in childhood astrocytomas by angiogenesis gene profiling. , 2003, Cancer research.

[54]  T. Golub,et al.  Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. , 2003, Cancer research.

[55]  E. Dougherty,et al.  Identification of combination gene sets for glioma classification. , 2002, Molecular cancer therapeutics.

[56]  M. Teh,et al.  FOXM1 is a downstream target of Gli1 in basal cell carcinomas. , 2002, Cancer research.

[57]  Mark R Gilbert,et al.  Gene expression microarray analysis reveals YKL-40 to be a potential serum marker for malignant character in human glioma. , 2002, Cancer research.

[58]  Shuichi Tsutsumi,et al.  Distinction in gene expression profiles of oligodendrogliomas with and without allelic loss of 1p , 2002, Oncogene.

[59]  T. Poggio,et al.  Prediction of central nervous system embryonal tumour outcome based on gene expression , 2002, Nature.

[60]  Van,et al.  A gene-expression signature as a predictor of survival in breast cancer. , 2002, The New England journal of medicine.

[61]  David E. Misek,et al.  Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. , 2001, Cancer research.

[62]  P. Black,et al.  Prognostic and pathologic significance of quantitative protein expression profiling in human gliomas. , 2001, Clinical cancer research : an official journal of the American Association for Cancer Research.

[63]  M. Watson,et al.  Gene expression profiling with oligonucleotide microarrays distinguishes World Health Organization grade of oligodendrogliomas. , 2001, Cancer research.

[64]  M. Kurrer,et al.  Gene expression profiling of low-grade diffuse astrocytomas by cDNA arrays. , 2000, Cancer research.

[65]  O. Kallioniemi,et al.  Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. , 2000, Cancer research.

[66]  Scar,et al.  Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. , 2000, The New England journal of medicine.

[67]  G. Fuller,et al.  Toward a molecular classification of the gliomas: histopathology, molecular genetics, and gene expression profiling. , 2000, Histology and histopathology.

[68]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[69]  W. Yung,et al.  Reactivation of insulin-like growth factor binding protein 2 expression in glioblastoma multiforme: a revelation by parallel gene expression profiling. , 1999, Cancer research.

[70]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[71]  D. Louis,et al.  Specific genetic predictors of chemotherapeutic response and survival in patients with anaplastic oligodendrogliomas. , 1998, Journal of the National Cancer Institute.

[72]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[73]  S. P. Fodor,et al.  Light-generated oligonucleotide arrays for rapid DNA sequence analysis. , 1994, Proceedings of the National Academy of Sciences of the United States of America.