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Array Comparative Genomic Hybridization pp 325–338Cite as

Array CGH in Brain Tumors

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 973))

Abstract

Alterations in the copy number of the cancer genome are frequently observed in brain tumors especially gliomas. Some pertinent examples include amplification of the EGFR locus in chromosome 7p and loss of the PTEN locus in 10q in glioblastoma. Meningiomas are often associated with loss of the NF2 locus in 22q. Array CGH or aCGH probes provide a reliable, consistent, and economical method of profiling genome-wide copy number alterations (CNAs) of cancer specimens at fairly robust resolution. This has allowed for the systematic assessment of brain tumors for recurrent genomic CNAs. In addition, recent technical advancements have increased the robustness of this technique to accommodate DNA derived from formalin-fixed paraffin-embedded (FFPE) tissue. Lastly, novel technologies such as next-generation sequencing and multiplex digital gene counting technology such as NanoString will expand the ­repertoire of techniques for assessing CNAs in brain tumors.

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References

  1. Iafrate AJ, Feuk L, Rivera MN et al (2004) Detection of large-scale variation in the human genome. Nat Genet 36(9):949–951. doi:10.1038/ng1416 ng1416 [pii]

    Article  PubMed  CAS  Google Scholar 

  2. Lee C, Iafrate AJ, Brothman AR (2007) Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 39(7 Suppl):S48–S54. doi:ng2092 [pii] 10.1038/ng2092

    Article  PubMed  CAS  Google Scholar 

  3. Sanders SJ, Ercan-Sencicek AG, Hus V et al (2011) Multiple recurrent de novo CNVs, including duplications of the 7q11.23 williams syndrome region, are strongly associated with autism. Neuron 70(5):863–885. doi:doi:S0896-6273(11)00374-6 [pii] 10.1016/j.neuron.2011.05.002

    Article  PubMed  CAS  Google Scholar 

  4. Stefansson H, Rujescu D, Cichon S et al (2008) Large recurrent microdeletions associated with schizophrenia. Nature 455(7210):232–236. doi:nature07229 [pii] 10.1038/nature07229

    Article  PubMed  CAS  Google Scholar 

  5. Weiss LA, Shen Y, Korn JM et al (2008) Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med 358(7):667–675. doi:NEJMoa075974 [pii] 10.1056/NEJMoa075974

    Article  PubMed  CAS  Google Scholar 

  6. Beroukhim R, Mermel CH, Porter D et al (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463(7283):899–905. doi:nature08822 [pii] 10.1038/nature08822

    Article  PubMed  CAS  Google Scholar 

  7. Ou Z, Stankiewicz P, Xia Z et al (2011) Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes. Genome Res 21(1):33–46. doi:gr.111609.110 [pii] 10.1101/gr.111609.110

    Article  PubMed  CAS  Google Scholar 

  8. Basinko A, Audebert-Bellanger S, Douet-Guilbert N et al (2011) Subtelomeric monosomy 11q and trisomy 16q in siblings and an unrelated child: molecular characterization of two der(11)t(11;16). Am J Med Genet A 155(9):2281–2287. doi:10.1002/ajmg.a.34162

    Article  CAS  Google Scholar 

  9. Nicholas MK, Lukas RV, Jafri NF et al (2006) Epidermal growth factor receptor—mediated signal transduction in the development and therapy of gliomas. Clin Cancer Res 12(24):7261–7270. doi:12/24/7261 [pii] 10.1158/1078-0432.CCR-06-0874

    Article  PubMed  CAS  Google Scholar 

  10. Hostetter G, Kim SY, Savage S et al (2010) Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples. Nucleic Acids Res 38(2):e9. doi:10.1093/nar/gkp881

    Article  PubMed  Google Scholar 

  11. Panzeri E, Conconi D, Antolini L et al (2011) Chromosomal aberrations in bladder cancer: fresh versus formalin fixed paraffin embedded tissue and targeted FISH versus wide microarray-based CGH analysis. PLoS One 6(9):e24237. doi:10.1371/journal.pone.0024237

    Article  PubMed  CAS  Google Scholar 

  12. Dutt A, Beroukhim R (2007) Single nucleotide polymorphism array analysis of cancer. Curr Opin Oncol 19(1):43–49

    Article  PubMed  CAS  Google Scholar 

  13. Meyerson M, Gabriel S, Getz G (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11(10):685–696. doi:nrg2841 [pii] 10.1038/nrg2841

    Article  PubMed  CAS  Google Scholar 

  14. Geiss GK, Bumgarner RE, Birditt B et al (2008) Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26(3):317–325. doi:10.1038/nbt1385

    Article  PubMed  CAS  Google Scholar 

  15. Payton JE, Grieselhuber NR, Chang LW et al (2009) High throughput digital quantification of mRNA abundance in primary human acute myeloid leukemia samples. J Clin Invest 119(6):1714–1726. doi:10.1172/JCI38248

    Article  PubMed  CAS  Google Scholar 

  16. Pinkel D, Segraves R, Sudar D et al (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20(2):207–211. doi:10.1038/2524

    Article  PubMed  CAS  Google Scholar 

  17. Snijders AM, Nowak N, Segraves R et al (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29(3):263–264. doi:10.1038/ng754

    Article  PubMed  CAS  Google Scholar 

  18. Cai WW, Mao JH, Chow CW et al (2002) Genome-wide detection of chromosomal imbalances in tumors using bac microarrays. Nat Biotechnol 20(4):393–396. doi:10.1038/nbt0402-393

    Article  PubMed  CAS  Google Scholar 

  19. Beheshti B, Braude I, Marrano P et al (2003) Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridization. Neoplasia 5(1):53–62

    PubMed  CAS  Google Scholar 

  20. Nigro JM, Misra A, Zhang L et al (2005) Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma. Cancer Res 65(5):1678–1686. doi:10.1158/0008-5472.CAN-04-2921

    Article  PubMed  CAS  Google Scholar 

  21. Mohapatra G, Engler DA, Starbuck KD et al (2011) Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas. Acta Neuropathol 121(4):529–543. doi:10.1007/s00401-010-0773-z

    Article  PubMed  CAS  Google Scholar 

  22. Gabeau-Lacet D, Engler D, Gupta S et al (2009) Genomic profiling of atypical meningiomas associates gain of 1q with poor clinical outcome. J Neuropathol Exp Neurol 68(10):1155–1165. doi:10.1097/NEN.0b013e3181ba3952 00005072-200910000-00011 [pii]

    Article  PubMed  CAS  Google Scholar 

  23. Olshen AB, Venkatraman ES, Lucito R et al (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5(4):557–572. doi:10.1093/biostatistics/kxh008

    Article  PubMed  Google Scholar 

  24. Korkola JE, Heck S, Olshen AB et al (2008) In vivo differentiation and genomic evolution in adult male germ cell tumors. Genes Chromosomes Cancer 47(1):43–55. doi:10.1002/gcc.20504

    Article  PubMed  CAS  Google Scholar 

  25. Van Wieringen WN, Van De Wiel MA, Ylstra B (2007) Normalized, segmented or called aCGH data? Cancer Inform 3:321–327

    PubMed  Google Scholar 

  26. Beroukhim R, Getz G, Nghiemphu L et al (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A 104(50):20007–20012. doi:10.1073/pnas.0710052104

    Article  PubMed  CAS  Google Scholar 

  27. Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061–1068. doi:nature07385 [pii] 10.1038/nature07385

    Article  Google Scholar 

  28. Louis DN, Ohgaki H, Wiestler OD et al (eds) (2007) Who classification of tumours of the central nervous system. IARC, Lyon

    Google Scholar 

  29. Wen PY, Kesari S (2008) Malignant gliomas in adults. N Engl J Med 359(5):492–507. doi:359/5/492 [pii] 10.1056/NEJMra0708126

    Article  PubMed  CAS  Google Scholar 

  30. Ohgaki H, Kleihues P (2007) Genetic pathways to primary and secondary glioblastoma. Am J Pathol 170(5):1445–1453

    Article  PubMed  CAS  Google Scholar 

  31. Kesari S, Ramakrishna N, Sauvageot C et al (2005) Targeted molecular therapy of malignant gliomas. Curr Neurol Neurosci Rep 5(3):186–197

    Article  PubMed  CAS  Google Scholar 

  32. Yip S, Iafrate AJ, Louis DN (2008) Molecular diagnostic testing in malignant gliomas: a practical update on predictive markers. J Neuropathol Exp Neurol 67(1):1–15. doi:10.1097/nen.0b013e31815f65fb

    Article  PubMed  CAS  Google Scholar 

  33. Jansen M, Mohapatra G, Betensky RA et al (2011) Gain of chromosome arm 1q in atypical meningioma correlates with shorter progression-free survival. Neuropathol Appl Neurobiol. doi:10.1111/j.1365-2990.2011.01222.x

    Google Scholar 

  34. Le LP, Nielsen GP, Rosenberg AE et al (2011) Recurrent chromosomal copy number alterations in sporadic chordomas. PLoS One 6(5):e18846. doi:10.1371/journal.pone.0018846

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Medicine, Massachusetts General Hospital, Boston, MA, USA

    Gayatry Mohapatra

  2. Division of Neurosurgery, Department of Surgery, Vancouver General Hospital, Vancouver, BC, Canada

    Julia Sharma

  3. Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, Canada

    Stephen Yip

  4. Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, BC, Canada

    Stephen Yip

Authors
  1. Gayatry Mohapatra
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  2. Julia Sharma
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  3. Stephen Yip
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Corresponding author

Correspondence to Stephen Yip .

Editor information

Editors and Affiliations

  1. , Dept. of Pathology & Lab. Medicine, The Ottawa Hospital, Smyth Road 501, Ottawa, K1H 8L6, Ontario, Canada

    Diponkar Banerjee

  2. , Dept. of Molecular Oncology, BC Cancer Agency, West 10th Avenue 675, Vancouver, V5T 4E6, British Columbia, Canada

    Sohrab P. Shah

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Mohapatra, G., Sharma, J., Yip, S. (2013). Array CGH in Brain Tumors. In: Banerjee, D., Shah, S. (eds) Array Comparative Genomic Hybridization. Methods in Molecular Biology, vol 973. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-281-0_20

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  • DOI: https://doi.org/10.1007/978-1-62703-281-0_20

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-280-3

  • Online ISBN: 978-1-62703-281-0

  • eBook Packages: Springer Protocols

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