title: Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA.
abstract: The ability to utilize formalin-fixed, paraffin-embedded (FFPE) archival specimens reliably for high-resolution molecular genetic analysis would be of immense practical application in the study of human disease. We have evaluated the ability of the GenomePlex whole genome amplification (WGA) kit to amplify frozen and FFPE tissue for use in array CGH (aCGH). GenomePlex gave highly representative data compared with unamplified controls both from frozen material (Pearson's R(2) = 0.898) and from FFPE (R(2) = 0.883). Artifactual amplification observed using DOP-PCR at chromosomes 1p, 3, 13q, and 16p was not seen with GenomePlex. Highly reproducible aCGH profiles were obtained using as little as 5 ng starting material from FFPE (R(2) = 0.918). This WGA method should readily lend itself to the determination of DNA copy number alterations from small fresh-frozen and FFPE clinical tumor specimens, although some care must be taken to optimize the DNA extraction procedure.
authors.affiliation: Paediatric Oncology, Institute of Cancer Research/Royal Marsden NHS Trust, Sutton, Surrey SM2 5NG, UK.
authors.forename: Suzanne E
authors.initials: SE
authors.lastname: Little
authors.forename: Raisa
authors.initials: R
authors.lastname: Vuononvirta
authors.forename: Jorge S
authors.initials: JS
authors.lastname: Reis-Filho
authors.forename: Rachael
authors.initials: R
authors.lastname: Natrajan
authors.forename: Marjan
authors.initials: M
authors.lastname: Iravani
authors.forename: Kerry
authors.initials: K
authors.lastname: Fenwick
authors.forename: Alan
authors.initials: A
authors.lastname: Mackay
authors.forename: Alan
authors.initials: A
authors.lastname: Ashworth
authors.forename: Kathy
authors.initials: K
authors.lastname: Pritchard-Jones
authors.forename: Chris
authors.initials: C
authors.lastname: Jones
mesh_terms: D004273:DNA, Neoplasm / Q000235:genetics*; D005557:Formaldehyde / Q000737:chemistry*; D016678:Genome; D006801:Humans; D009693:Nucleic Acid Hybridization; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D016707:Tissue Fixation
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde