Microarray-Based CGH and Copy Number Analysis of FFPE Samples

  • Fahd Al-MullaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 724)


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 words

Microarray 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.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Molecular Pathology UnitHealth Sciences CenterSafatKuwait

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