Abstract 3203: High quality DNA obtained with an automated DNA Extraction method with 15 to 40 year old formalin fixed paraffin embedded (FFPE) blocks from normal and cancer tissues

Abstract

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL DNA and RNA have been used as markers of tissue quality and integrity in tissues the last decade. In this research study, kidney, liver, colon, lung, and breast genomic quality were analyzed in tissues from surgical cancer patients and post-mortem cases obtained with an IRB approved protocol and informed/or next of kin consent. DNA extraction was performed on formalin-fixed paraffin-embedded tissues (FFPE) from both groups of cases from the 1970's through the 2000's and formalin fixed / long term 70% ethanol storage(15 + years). To extract the DNA from the FFPE tissues, we soaked all tissues in xylene to remove the paraffin, digested the tissue with a proteinase K solution, and used an automated extraction machine to extract the DNA. A similar SOP was used for the formalin fixed/ 70% long term ethanol-stored tissue, except the tissue was first homogenized rather than soaked in xylene. DNA quality and yield were evaluated using a spectrophotometer. Gel electrophoresis was used to evaluate the length of the DNA in about 20% of the 200 samples. Samples that had optical density (OD) readings above 1.60 and below 2.10 with a DNA yield above 100 µg/mL were deemed to be high quality DNA. FFPE tissues yielded the highest DNA concentration and quality (OD reading of 1.87 and yield of 625 ug/ml) with greater than 95% of the samples meeting the above specifications, while the formalin fixed/long term 70% ethanol stored tissue yielded both the lowest DNA concentration and quality (yield of 52 ug/ml and OD reading of 1.48). In conclusion, the results show that high quality DNA can be extracted from FFPE tissue using an automated DNA extraction procedure with paraffin blocks from the early 1970's to present, and the DNA extracted is useful for clinical and experimental studies. The DNA from tissues stored in aqueous media (formalin fixed / long term 70% ethanol storage) may be useful in some research applications, but the DNA is partially degraded compared to the tissue stored in paraffin blocks. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3203. doi:1538-7445.AM2012-3203