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

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

Research output: Contribution to journalArticle

54 Citations (Scopus)

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
StatePublished - Feb 2005
Externally publishedYes

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Comparative Genomic Hybridization
Paraffin
Formaldehyde
Breast Neoplasms
DNA
Oligonucleotides
Genome
Oligonucleotide Array Sequence Analysis
Polymerase Chain Reaction
Neoplasms

ASJC Scopus subject areas

  • Molecular Biology

Cite this

DeVries, S., Nyante, S., Korkola, J., Segraves, R., Nakao, K., Moore, D., ... Waldman, F. (2005). Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. Journal of Molecular Diagnostics, 7(1), 65-71.

Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. / DeVries, Sandy; Nyante, Sarah; Korkola, James; Segraves, Richard; Nakao, Kentaro; Moore, Dan; Bae, Hanik; Wilhelm, Monica; Hwang, Shelley; Waldman, Frederic.

In: Journal of Molecular Diagnostics, Vol. 7, No. 1, 02.2005, p. 65-71.

Research output: Contribution to journalArticle

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, vol. 7, no. 1, pp. 65-71.
DeVries, Sandy ; Nyante, Sarah ; Korkola, James ; Segraves, Richard ; Nakao, Kentaro ; Moore, Dan ; Bae, Hanik ; Wilhelm, Monica ; Hwang, Shelley ; Waldman, Frederic. / Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. In: Journal of Molecular Diagnostics. 2005 ; Vol. 7, No. 1. pp. 65-71.
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