Abstract 3178: Can DNA from archived formalin-fixed paraffin embedded (FFPE) cancer tissues be used for somatic mutation analysis in next generation sequencing

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Formalin-fixed paraffin embedded (FFPE) tissues are far more abundant in most tissue banks and pathology departments than fresh or fresh frozen (FF) samples, but typically yield varying degrees of degraded DNA as a result of the fixation process. The quality of FFPE tissues may vary based on a number of factors such as: age of the block, fixation time, storage and handling conditions. Being able to harness the power of next generation sequencing technologies to genomically characterize these abundant and diverse achieved samples would be tremendously valuable to the cancer research community and would enable the use of this material for clinical purposes. The goal of this study was to assess the performance of FFPE samples in next generation sequencing applications. We monitored close to 100 samples from tumor and normal tissues of FFPE, FF and blood origin. These samples underwent several processes for whole-exome or targeted sequencing, including DNA fragmentation, size selection, library preparation, and hybrid-capture enrichment. We observed variable performance across these samples at several of the above steps, which correlated predominantly with FFPE tissues and the age of block. Other quality metrics that showed relative lower performance of FFPE DNA were the cluster density, duplication rate or library complexity. Most FFPE samples still generated good quality sequence, however, older FFPE blocks, over 10 years, may need more input DNA or higher sequence depth to reach minimum coverage if somatic mutation analysis is the goal. There was no difference in performance between DNA from tumor and normal tissues. 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 3178. doi:1538-7445.AM2012-3178