Microarray-Based CGH and Copy Number Analysis of FFPE Samples
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Over the past decade, utilization of microarray technology has flourished in biomedical research. It has evolved rapidly into a revolutionary tool that offers deeper insight into the molecular basis associated with complex diseases, especially in the field of cancer. Specifically, array-based Comparative Genomic Hybridization (aCGH) permits the detection of genome-wide copy number alterations with high resolution. Microarray application to DNA extracted from formalin-fixed paraffin-embedded tissue (FFPE), in particular, poses a challenge due to the partially degraded nature and compromised quality of the DNA. This chapter gives a description of the several CGH-microarray platforms currently available and offers practical steps that guide you through optimal handling and superior aCGH data acquisition of DNA extracted from FFPE tissues.
Key wordsMicroarray Array-based comparative genomic hybridization Formalin-fixed paraffin embedded Copy number Microarray platforms Copy number variation
This work is supported by Kuwait Foundation for the Advancement of Sciences grant number 2006-1302-07, Kuwait University Grant number MG02/08 and Research Core Facility (RCF) grant number GM 01/01 and GM 01/05. Thanks go to Dian Ann Thomas for her excellent technical skills.
- 5.Hardiman, G. (2004) Microarray platforms: comparisons and contrasts. Pharmacogenetics 5, 487–502.Google Scholar
- 9.http://www.agilent.com User Guide. © Agilent Technologies, Inc. 2007.
- 10.Hostetter, G., Kim, S. Y., Savage, S., Gooden, G.C., Barrett, M., Zhang, J., 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 Research 38, e9.PubMedCrossRefGoogle Scholar