Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors.

Journal Article (Journal Article)

Identification of prognostic and predictive genomic markers requires long-term clinical follow-up of patients. Extraction of high-quality DNA from archived formalin-fixed, paraffin-embedded material is essential for such studies. Of particular importance is a robust reproducible method of whole genome amplification for small tissue samples. This is especially true for high-resolution analytical approaches because different genomic regions and sequences may amplify differentially. We have tested a number of protocols for DNA amplification for array-based comparative genomic hybridization (CGH), in which relative copy number of the entire genome is measured at 1 to 2 mb resolution. Both random-primed amplification and degenerate oligonucleotide-primed amplification approaches were tested using varying amounts of fresh and paraffin-extracted normal and breast tumor input DNAs. We found that random-primed amplification was clearly superior to degenerate oligonucleotide-primed amplification for array-based CGH. The best quality and reproducibility strongly depended on accurate determination of the amount of input DNA using a quantitative polymerase chain reaction-based method. Reproducible and high-quality results were attained using 50 ng of input DNA, and some samples yielded quality results with as little as 5 ng input DNA. We conclude that random-primed amplification of DNA isolated from paraffin sections is a robust and reproducible approach for array-based CGH analysis of archival tumor samples.

Full Text

Duke Authors

Cited Authors

  • Devries, S; Nyante, S; Korkola, J; Segraves, R; Nakao, K; Moore, D; Bae, H; Wilhelm, M; Hwang, S; Waldman, F

Published Date

  • February 2005

Published In

Volume / Issue

  • 7 / 1

Start / End Page

  • 65 - 71

PubMed ID

  • 15681476

Pubmed Central ID

  • PMC1867501

International Standard Serial Number (ISSN)

  • 1525-1578

Digital Object Identifier (DOI)

  • 10.1016/S1525-1578(10)60010-4


  • eng

Conference Location

  • United States