Abstract 427: High-quality whole-genome sequencing of FFPE samples

Next-generation sequencing analysis of formalin-fixed, paraffin-embedded (FFPE) samples has the potential to lead to major advances in cancer treatment and prevention. However, whole-genome sequencing of these samples has remained challenging due to the difficult process of isolating high-quality DNA and distinguishing true variant calls from artifacts. Previous studies have attempted to overcome these challenges by using whole-exome sequencing or smaller exon panels at high coverage depths to analyze FFPE samples. While these approaches have produced useful results, they have had varying degrees of success, tend have coverage biases due to probe capture issues, and are limited to only a fraction of the genome. Thus, there has not been widespread adoption of using FFPE samples for next-generation sequencing. In an attempt to improve on the process of next-generation sequencing of FFPE samples, we first developed an efficient DNA extraction method that produces high quantities of high-quality DNA. Whole-genome sequencing of DNA generated by this method demonstrated uniform high coverage that was comparable to DNA prepared from fresh frozen samples at the same sequencing depth. This result is in contrast with data generated from DNA isolated by a traditional FFPE extraction method, which had lesser sequencing coverage even with twice the sequencing depth. Further analysis of the data generated using our method demonstrated similar numbers of mutations called and mutational signatures without artifact contamination. We extended this analysis to a large cancer cohort consisting of over 1,000 FFPE samples in tumor normal pairs that were up to 6 years old. Whole-genome sequencing of these samples demonstrate that there was an average of 98% of the genome covered at 20X or greater using our method with no drop off for the older samples. Mutational analyses of these samples demonstrate similar findings as that previously published using TCGA datasets. In summary, our study of greater than 1,000 samples is the largest report of whole-genome sequencing of FFPE samples to date. Our results demonstrate the feasibility of using our method to assay tissues stored in archival tissue biobanks, analyze patient samples for clinical trial recruitment, or examining sections as part of normal clinical workflows, all of which hold the potential for greatly benefiting human health. Citation Format: Shannon T. Bailey, Jim Lund, Hao Wang, Weiren Cui, Chen Hao, Hongye Sun, Jeffrey R. Gulcher. High-quality whole-genome sequencing of FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 427.