Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA.
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.
Little
Suzanne E
SE
Paediatric Oncology, Institute of Cancer Research/Royal Marsden NHS Trust, Sutton, Surrey SM2 5NG, UK.
Vuononvirta
Raisa
R
Reis-Filho
Jorge S
JS
Natrajan
Rachael
R
Iravani
Marjan
M
Fenwick
Kerry
K
Mackay
Alan
A
Ashworth
Alan
A
Pritchard-Jones
Kathy
K
Jones
Chris
C
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
D004273:DNA, Neoplasm; D005557:Formaldehyde