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

doi:10.1016/s1525-1578(10)60010-4

PubMed · 15681476

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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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.

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Breast Neoplasms DNA, Neoplasm Female Fixatives Formaldehyde Humans Nucleic Acid Amplification Techniques Oligonucleotide Array Sequence Analysis Paraffin Embedding Prognosis Reproducibility of Results Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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Sandy Devries, Sarah Nyante, Jim Korkola, Richard Segraves, Kentaro Nakao, Dan Moore, Hanik Bae, Monica Wilhelm, Shelley Hwang, Frederic Waldman. 2005. Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors.. https://doi.org/10.1016/s1525-1578(10)60010-4

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