NCI SEER Formalin Fixed Paraffin Embedded (FFPE) Tissue Feasibility Study

Next Generation Sequencing (NGS) technologies are being used for detection of somatic mutations in tumors and studies of germline variation. However, most NGS studies used DNA isolated either from whole blood or fresh frozen tissue specimens. Meanwhile, the tissue specimens available from most National Cancer Institute (NCI) funded cohorts and the Surveillance, Epidemiology and End Results (SEER) registries (http://seer.cancer.gov/biospecimen) are primarily formalin fixed paraffin embedded (FFPE). There are limited data, on a small number of FFPE tissue samples, which suggest NGS is feasible. Much less is known about the feasibility of these technologies for large scale studies or using older FFPE specimens (e.g. 5-30 years old). The SEER cancer registries cover approximately 28% of the United States population, providing high quality demographic, clinical, pathologic, and survival data. The SEER Residual Tissue Repository (RTR) program was established in 2003. The RTR maintains biospecimens obtained from three of SEER' population-based cancer registries: Iowa, Hawaii, and Los Angeles. Investigators at government, academic, and nonprofit institutions may apply to the program to obtain annotated FFPE tumor tissue specimens to study biomarkers, etiology, and other aspects with a population-based sample of cancer cases. The main objective of this project was to conduct a pilot study to determine whether the DNA obtained from archival FFPE tissue from 3 SEER Registries is of sufficient quality and quantity to conduct NGS. For Exome sequencing, sixty high-grade serous ovarian adenocarcinomas from FFPE tissues which were between 7 and 31 years old were obtained from three SEER registries. DNA was extracted, quantified, quality assessed, and subjected to whole exome sequencing. DNA extraction (yields and quality) and whole exome sequencing (depths of coverage and exome coverage obtained) results from this study will be presented. For RNA-sequencing, sixty-seven high-grade serous ovarian adenocarcinomas from FFPE tissues which were between 7 and 31 years old were obtained from three SEER registries. Total RNA was extracted, quantified, quality assessed, and subjected to whole transcriptome sequencing. Ultimately data derived from this analysis could serve as the basis for determining the utility of archival FFPE biospecimens for characterization and discovery projects utilizing NGS technologies instead of relying on frozen biospecimens. ]]>
As specimens were retrospectively collected from multiple medical facilities and pathology labs, fixation times/conditions and storage conditions were unknown. Tissues were from high-grade serous ovarian adenocarcinomas (ICD-O-3 Topography code: C56.9; Morphology codes: 8441/3, 8460/3, 8461/3) and storage time ranged from 3 to 32 years ( see Table below) based on decade when tissue was resected. Table Exome and RNA-seq Specimen Storage Time Specimen Storage Time 3-12 years 13-22 years 23-32 years No information about storage time SEER site 1 8 9 3 0 SEER site 2 4 11 5 0 SEER site 3 1 11 7 1 Total 13 31 15 1 ]]>
The SEER registries are population-based and collect data on all cancer cases in their geographic areas. The types of information that may be available include: demographic information tumor characteristics limited treatment data survival and cause of death Thus, the SEER registries provide a unique opportunity for performing biospecimen studies on a representative sample of cancer cases from a particular geographic area. Recognizing this potential, the SEER Residual Tissue Repository (RTR) program was established in 2003. The RTR program aims to retain specimens associated with SEER patients that would otherwise be discarded. Investigators can use these specimens for research on prognostic biomarkers, etiology, and other hypotheses relevant to the population-based sample. Most RTR biospecimens are formalin-fixed paraffin-embedded tissue blocks; however, some other biospecimens are maintained within the RTR. The RTR: Enables studies on rare cancers by drawing from multiple registries to increase statistical power. Allows validation studies on specimens from population-based registries. Allows evaluation of bias within tumor collections since the SEER database provides information on all cancer cases in the registry catchment. Makes available the wealth of SEER data on each cancer. Allows analysis of trends in incidence, survival and treatment over the history and diversity of the SEER registries. Permits updating of survival data after a tissue microarray (TMA) is formed without violating privacy protections. ]]>