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Biomarkers in Neoplastic Neuropathology

Abstract

One of the main advantages of cancer research and the field of biomarker discovery is the public availability of high-throughput data on an unparalleled scale. This has been made possible by the availability of public, user-friendly databases that allow the mining of large molecular datasets with ease. The Cancer Genome Atlas (TCGA) effort, pioneered in the study of brain cancer (glioblastoma), has also become a priceless resource for neoplastic neuropathology and has fueled numerous efforts in the generation and testing of specific hypotheses and biomarker discovery. Currently, TCGA has completed comprehensive molecular profiling of glioblastomas and lower-grade gliomas (diffuse gliomas grades II–III), the most important group of primary brain tumors in adults.

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References

  1. Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061–1068

    Article  Google Scholar 

  2. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P et al (2008) An integrated genomic analysis of human glioblastoma multiforme. Science [Research Support, NIH, Extramural Research Support, Non-US Gov’t] 321(5897):1807–1812

    CAS  Google Scholar 

  3. Watanabe T, Nobusawa S, Kleihues P, Ohgaki H (2009) IDH1 mutations are early events in the development of astrocytomas and oligodendrogliomas. Am J Pathol [Research Support, Non-US Gov’t] 174(4):1149–1153

    CAS  Google Scholar 

  4. Yan H, Parsons DW, Jin G, McLendon R, Rasheed BA, Yuan W et al (2009) IDH1 and IDH2 mutations in gliomas. N Engl J Med [Research Support, NIH, Extramural Research Support, Non-US Gov’t] 360(8):765–773

    CAS  Google Scholar 

  5. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR et al (2013) The somatic genomic landscape of glioblastoma. Cell 155(2):462–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Cancer Genome Atlas Research N, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR et al (2015) Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. N Engl J Med [Research Support, NIH, Extramural] 372(26):2481–2498

    Google Scholar 

  7. Eckel-Passow JE, Lachance DH, Molinaro AM, Walsh KM, Decker PA, Sicotte H et al (2015) Glioma groups based on 1p/19q, IDH, and TERT promoter mutations in tumors. N Engl J Med [Research Support, NIH, Extramural Research Support, Non-US Gov’t] 372(26):2499–2508

    CAS  Google Scholar 

  8. Gorovets D, Kannan K, Shen R, Kastenhuber ER, Islamdoust N, Campos C et al (2012) IDH mutation and neuroglial developmental features define clinically distinct subclasses of lower grade diffuse astrocytic glioma. Clin Cancer Res [Research Support, Non-US Gov’t] 18(9):2490–2501

    Article  CAS  Google Scholar 

  9. Madhavan S, Zenklusen JC, Kotliarov Y, Sahni H, Fine HA, Buetow K (2009) Rembrandt: helping personalized medicine become a reality through integrative translational research. Mol Cancer Res [Research Support, NIH, Intramural] 7(2):157–167

    CAS  Google Scholar 

  10. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA et al (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov [Research Support, NIH, Extramural Research Support, Non-US Gov’t] 2(5):401–404

    Google Scholar 

  11. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO et al (2013) Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal [Research Support, NIH, ExtramuralResearch Support, Non-US Gov’t] 6(269):pl1

    Google Scholar 

  12. Reva B, Antipin Y, Sander C (2011) Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res [Research Support, NIH, Extramural Validation Studies] 39(17):e118

    CAS  Google Scholar 

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Rodriguez, F., Ho, CY. (2016). Public Databases. In: Biomarkers in Neoplastic Neuropathology. Springer, Cham. https://doi.org/10.1007/978-3-319-20931-9_4

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  • DOI: https://doi.org/10.1007/978-3-319-20931-9_4

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-20930-2

  • Online ISBN: 978-3-319-20931-9

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