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Genomic analysis by oligonucleotide array comparative genomic hybridization utilizing formalin-fixed, paraffin-embedded tissues

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Abstract

Formalin fixation has been used to preserve tissues for more than a hundred years, and there are currently more than 300 million archival samples in the United States alone. The application of genomic protocols such as high-density oligonucleotide array Comparative Genomic Hybridization (aCGH) to formalin-fixed, paraffin-embedded (FFPE) tissues, therefore, opens an untapped resource of available tissues for research and facilitates utilization of existing clinical data in a research sample set. However, formalin fixation results in cross-linking of proteins and DNA, typically leading to such a significant degradation of DNA template that little is available for use in molecular applications. Here, we describe a protocol to circumvent formalin fixation artifact by utilizing enzymatic reactions to obtain quality DNA from a wide range of FFPE tissues for successful genome-wide discovery of gene dosage alterations in archival clinical samples. © 2011 Springer Science+Business Media, LLC.

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Savage, S. J., & Hostetter, G. (2011). Genomic analysis by oligonucleotide array comparative genomic hybridization utilizing formalin-fixed, paraffin-embedded tissues. Methods in Molecular Biology, 700, 185–198. https://doi.org/10.1007/978-1-61737-954-3_13

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