title: Genomic analysis by oligonucleotide array Comparative Genomic Hybridization utilizing formalin-fixed, paraffin-embedded tissues.
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.
authors.affiliation: Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
authors.forename: Stephanie J
authors.initials: SJ
authors.lastname: Savage
authors.forename: Galen
authors.initials: G
authors.lastname: Hostetter
mesh_terms: D055028:Comparative Genomic Hybridization; D005557:Formaldehyde / Q000737:chemistry*; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D016612:Paraffin Embedding; D016707:Tissue Fixation
chemical_list: D005557:Formaldehyde