Although fresh frozen tissue is the optimal source of nucleic acids for sequencing, obtaining such tissue on a population scale is cost and time prohibitive; however, DNA and RNA extraction from formalin-fixed, paraffin-embedded (FFPE) tissue has been problematic, yielding low quantity and quality DNA and RNA. Through a pilot program, the National Cancer Institute is developing a Surveillance, Epidemiology and End Results (SEER)-linked Virtual Tissue Repository (VTR) for obtaining deidentified FFPE tissue and clinical history. One such pancreatic ductal adenocarcinoma (PDAC) pilot project requested FFPE tumor and normal tissue (duodenum, lymph node, or spleen) and clinical history data on 24 matched pairs, comparing PDAC patients who survived at least five years since diagnosis with patients who died within two years through six SEER registries. A pancreatic pathologist annotated H&E stained slides for tissue dissection of corresponding unstained tumor (DNA and RNA) and normal (DNA only) tissue slides. More than 30% of tumor and normal tissue specimens had DNA with high quality for sequencing (≥20% amplifiable DNA), and the majority of DNA samples had medium to high quality (amplifiable DNA ≥ 10%) for sequencing. Although less DNA (quantity) was obtained from tumor tissue than normal, the percent amplifiable DNA was similar. DNA quantity was independent of tissue age (4 to 18 years); however, DNA integrity number (DIN) was significantly decreased in older tissue. Although RNA quantity was independent of tissue age, RNA quality (DV200) was significantly decreased in older tissue. There was no significant association between RNA quantity and quality. From the 24 pairs, sufficient DNA was obtained for whole genome sequencing (WGS) for 14 pairs, whole exome sequencing (WES) for eight pairs, and methylation studies on three pairs. Four pairs that had cases with <100 ng of tumor DNA were not included in the WGS. WGS, WES, methylation studies, and RNASeq are underway, and sequencing quality assessments will be performed. In a future expansion of this pilot project, deidentified tissue and clinical history will be obtained from an additional 76 patient pairs. Our study provided important evidence for understanding the DNA and RNA quantity and quality yields from archival PDAC FFPE tissue specimens with different ages at the population level. These findings also support the adequacy of FFPE tissue specimens for molecular studies and establish the feasibility of a population-based, SEER-linked VTR.
Citation Format: Yao Yuan, Alison Van Dyke, Valentina Petkov, Aatur Singhi, William Hoos, Lola Rahib, Lynn Matrisian, Lynne Penberthy. DNA and RNA from formalin-fixed, paraffin-embedded pancreatic cancer tissue for sequencing: A pilot study of the SEER-linked Virtual Tissue Repository [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-177.