Abstract
The characterization of molecular alterations specific to cancer facilitates the discovery of predictive and prognostic biomarkers important to targeted therapeutics. Alterations critical to cancer therapeutics include copy number alterations (CNAs) such as gene amplifications and deletions as well as genomic rearrangements resulting in gene fusions. There are two genome-wide technologies used to detect CNAs: next generation sequencing (NGS) and dense microarray based comparative genomic hybridization, termed array CGH (aCGH). aCGH is a mature robust technology of lower cost and more accessible than NGS. This chapter describes the protocol steps and analysis required to obtain reliable aCGH results from clinical samples. Technical options and various necessary compromises related to the nature of clinical material are considered and the consequences of these choices for data analysis and interpretation are discussed. The chapter includes brief description of the data analysis, even though analysis is often performed by bioinformaticians. Today’s cancer research requires collaboration of clinicians, molecular biologists, and mathematicians. Acquaintance with the basic principles related to the extraction of the data from arrays, its normalization and the algorithms available for analysis provides a baseline for mutual understanding and communication.
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References
Ross JS, Fletcher JA, Bloom KJ et al (2004) Targeted therapy in breast cancer: the HER-2/neu gene and protein. Mol Cell Proteomics 3:379–398
Shigematsu H, Gazdar AF (2006) Somatic mutations of epidermal growth factor receptor signaling pathway in lung cancers. Int J Cancer 118:257–262
Mano H (2008) Non-solid oncogenes in solid tumors: EML4-ALK fusion genes in lung cancer. Cancer Sci 99:2349–2355
Neal JW, Sequist LV (2010) Exciting new targets in lung cancer therapy: ALK, IGF-1R, HDAC, and Hh. Curr Treat Options Oncol 11:36–44
Meyerson M, Gabriel S, Getz G (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11:685–696
Pinkel D, Albertson DG (2005) Array comparative genomic hybridization and its applications in cancer. Nat Genet 37(Suppl):S11–S17
Curtis C, Lynch AG, Dunning MJ et al (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10:588
Przybytkowski E, Ferrario C, Basik M (2011) The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome. BMC Med Genomics 4:16
Pinto D, Darvishi K, Shi X et al (2011) Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 29:512–520
Klopfleisch R, Weiss AT, Gruber AD (2011) Excavation of a buried treasure–DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues. Histol Histopathol 26:797–810
Navin N, Kendall J, Troge J et al (2011) Tumour evolution inferred by single-cell sequencing. Nature 472:90–94
Callagy G, Jackson L, Caldas C (2005) Comparative genomic hybridization using DNA from laser capture microdissected tissue. Methods Mol Biol 293:39–55
Ruiz C, Lenkiewicz E, Evers L et al (2011) Advancing a clinically relevant perspective of the clonal nature of cancer. Proc Natl Acad Sci USA 108:12054–12059
Navin N, Krasnitz A, Rodgers L et al (2010) Inferring tumor progression from genomic heterogeneity. Genome Res 20:68–80
Hughes S, Lasken R (2005) Whole genome amplification. Scion Publishing Ltd, Bloxham
Hughes S, Lim G, Beheshti B et al (2004) Use of whole genome amplification and comparative genomic hybridisation to detect chromosomal copy number alterations in cell line material and tumour tissue. Cytogenet Genome Res 105:18–24
Pugh TJ, Delaney AD, Farnoud N et al (2008) Impact of whole genome amplification on analysis of copy number variants. Nucleic Acids Res 36:e80
Agilent Technology, Inc. Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells, or Tissues (with a High Throughput option) Protocol (February 2010) #G4410-90010_CGH_Enzymatic_Protocol_v6.2.1.pdf
Agilent Technology, Inc. Agilent Feature Extraction Software (v10.7) Reference Guide (October 2009) #G4460-90026_FE_Reference.pdf
Agilent Technology, Inc. Agilent Feature Extraction Software (v10.5) User Guide (december 2008) #G4460-90019_FE_10.5_User.pdf
Agilent Technology, Inc. http://www.genomics.agilent.com/GenericA.aspx?pagetype=Custom&subpagetype=Custom&pageid=2151,resourceontheweb
Agilent Technology, Inc. Agilent Genomic Workbench 6.5 CGH Interactive Analysis User Guide (September 2010) #g3800-90028_cgh_interactive.pdf
Hicks J, Krasnitz A, Lakshmi B et al (2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 16:1465–1479
Stankiewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61:437–455
Speleman F, Kumps C, Buysse K et al (2008) Copy number alterations and copy number variation in cancer: close encounters of the bad kind. Cytogenet Genome Res 123:176–182
Prensner JR, Chinnaiyan AM (2009) Oncogenic gene fusions in epithelial carcinomas. Curr Opin Genet Dev 19:82–91
Hampton OA, Den Hollander P, Miller CA et al (2009) A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res 19:167–177
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Przybytkowski, E., Aguilar-Mahecha, A., Nabavi, S., Tonellato, P.J., Basik, M. (2013). Ultradense Array CGH and Discovery of Micro-Copy Number Alterations and Gene Fusions in the Cancer Genome. 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_2
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DOI: https://doi.org/10.1007/978-1-62703-281-0_2
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