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Unlocking Clinical Tissue Archives to Genomic Analysis

Hospital tissue repositories contain valuable collections of formalin-fixed paraffin-embedded (FFPE) archival tissue blocks, with matched clinical information, that can serve as a rich resource for retrospective discovery studies. Though often challenging to analyze, a benefit of FFPE specimens is often both tumor and normal tissues from the same patient are available, facilitating identification of disease-relevant molecular signatures and genomic variations. Dr. Bauke Ylstra from the VU University Medical Center, Amsterdam, The Netherlands and colleagues describe protocols to acquire high-quality DNA from FFPE tissues, enabling identification of copy number aberrations by array comparative genomic hybridization (aCGH)1,2 . Especially critical steps in the procedure include removal of formalin-generated DNA cross-links and column-based DNA purification, rather than phenol/chloroform extraction, to avoid inhibition of enzymatic reactions in labeling and amplification steps. Using Enzo’s CGH labeling kit, the authors demonstrated analysis of FFPE samples was feasible for different high-resolution platforms (NimbleGen 135K aCGH, Agilent 180K aCGH), with reproducible results achieved even for low amounts of input DNA (50-100 ng).

Enzo Life Sciences’ CGH Labeling Kits generate high quality data using 250 ng or less genomic DNA, without need for pre-amplification. The BioScore™ Screening and Amplification kit is a rapid and reliable method to determine the quality of genomic DNA isolated from FFPE tissue samples prior to array CGH genome-wide copy number analysis and other genomic profiling applications.

(1.) Krijgsman et al (2012) “CGH Arrays Compared for DNA Isolated fromFormalin-Fixed, Paraffin-Embedded Material.” Genes Chromosomes Cancer. 51(4):344-52
(2.) van Essen and Ylstra (2012) “High-Resolution Copy Number Profiling by Array CGH Using DNA Isolated from Formalin-Fixed, Paraffin-Embedded Tissues.” In: Genomic Structural Variants: Methods and Protocols (Lars Feuk, ed.), Methods in Molecular Biology, vol. 838, pp 329-341


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