Copy-Number Analysis of Topoisomerase and Thymidylate Synthase Genes in Frozen and FFPE DNAs of Colorectal Cancers
- 14 October 2008
- journal article
- Published by Taylor & Francis Ltd in Pharmacogenomics
- Vol. 9 (10), 1459-1466
- https://doi.org/10.2217/14622416.9.10.1459
Abstract
Background: Archived formalin-fixed, paraffin-embedded specimens represent an important resource for pharmacogenomic analysis in retrospective clinical studies but the quality of results from formalin-fixed, paraffin-embedded samples is of concern due to the fact of the degradation of DNAs and RNAs from formalin-fixed, paraffin-embedded tissues. Methods: In the present study, we used DNA from fresh frozen as well as formalin-fixed, paraffin-embedded tumor to detect copy-number changes in colorectal cancer, and our data shows that formalin-fixed, paraffin-embedded DNAs were able to deliver reliable copy-number data, and that quantitative PCR had the ability to detect copy-number changes from deletion to amplification, with high concordance of copy-number calls among formalin-fixed, paraffin-embedded and frozen DNAs. Results: The amplification of topoisomerase I and deletion of thymidylate synthase were found in 23% (12/52) and 27% (14/52) of colorectal cancers, but EGF receptor amplification was not common...Funding Information
- National Institutes of Health (U01 GM63340, R21 CA102461, P30 CA091842)
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