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.
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Acknowledgments
The authors would like to recognize Gerald C. Gooden, Su Young Kim, Aprill Watanabe and Michael Syring for protocol development and design, and the collaborative efforts of Dr. Michael Bittner’s lab in protocol customization.
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Savage, S.J., Hostetter, G. (2011). Genomic Analysis by Oligonucleotide Array Comparative Genomic Hybridization Utilizing Formalin-Fixed, Paraffin-Embedded Tissues. In: DiStefano, J. (eds) Disease Gene Identification. Methods in Molecular Biology, vol 700. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61737-954-3_13
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DOI: https://doi.org/10.1007/978-1-61737-954-3_13
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Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61737-953-6
Online ISBN: 978-1-61737-954-3
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