Abstract 3585: Taqman genotyping assays can be used on decalcified and paraffin embedded tissue from patients with osteosarcoma

Abstract

Abstract Insight in genetic variants predicting treatment outcome and/or side effects related to cancer medication will contribute to optimize treatment for the individual patients. However, most clinical trials performed so far in cancer treatment did not routinely collect and store patient germ line DNA. Formalin-fixed paraffin-embedded tissues (FFPE) from archived clinical samples could provide a source of germ line DNA for genetic research. Specially, in cancers like osteosarcoma with a 5-year overall survival of approximately 50-60%, archived histological specimens are often the only accessible source of biological material. This material, however, generally has been decalcified and paraffin-embedded for many years. DNA from formalin-fixed and paraffin embedded (FFPE) tissues, specially, in decalcified FFPE tissues has a higher frequency of non-reproducible sequence alterations compared with germ line DNA. In our study, we investigated whether DNA obtained from these tissues can be used for reliable single nucleotide polymorphism (SNP) genotyping. Therefore, we analyzed whether the genotypes obtained from DNA of these preserved tissues, were similar as those found in freshly DNA isolated from peripheral blood cells from the same patients. We studied two SNPs in the drug transporter MDR1 (ABCB1) using Taqman® SNP genotyping assays. Genotypes of the germ line DNA derived from freshly isolated DNA of 20 surviving patients with osteosarcoma were compared with genotypes obtained from archived material from decalcified FFPE blocks of the same patients. Decalcified FFPE-derived DNA yielded smaller PCR fragments compared to DNA extracted from peripheral blood cells, with a maximum reliable size of ∼300bp. We were able to evaluate each SNP in 19 of the 20 cases included in this study. All successfully genotyped samples showed 100%-concordance between genotypes obtained from DNA of FFPE tissue and the genotypes obtained from DNA of blood. In conclusion, we have demonstrated that decalcified FFPE tissue can be used for genetic polymorphism analysis using Taqman® allelic discrimination assays. This forms an unique opportunity to combine new insights in genetic research with historical patient cohorts, for instance of patients with osteosarcoma. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3585.