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

Sandy DeVries, Sarah Nyante, Jim Korkola, Richard Segraves, Kentaro Nakao, Dan Moore, Hanik Bae, Monica Wilhelm, Shelley Hwang, Frederic Waldman

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54 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)65-71
Number of pages7
JournalJournal of Molecular Diagnostics
Volume7
Issue number1
DOIs
StatePublished - Feb 2005

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ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

Cite this

DeVries, S., Nyante, S., Korkola, J., Segraves, R., Nakao, K., Moore, D., Bae, H., Wilhelm, M., Hwang, S., & Waldman, F. (2005). Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. Journal of Molecular Diagnostics, 7(1), 65-71. https://doi.org/10.1016/S1525-1578(10)60010-4