Abstract 4695: Development and validation of an accurate exome-scale cfDNA detection platform
Authors: Simo V. Zhang, Charles Abbott, Robin Li, Eric Levy, Shujun Luo, Robert Power, Rena McClory, John West, Richard Chen, Sean Michael Boyle
Journal: Cancer Research (2019)

Abstract Background: Neoantigens are increasingly critical as biomarkers for immunotherapy response to checkpoint blockade therapy and as therapeutic targets for neoantigen-based personalized cancer vaccines. Accurate identification of neoantigens requires comprehensive exome and transcriptome sequencing of both a tumor biopsy and the matched normal samples to enable identification of putative neoantigens - which occur across the genome. Methods: However, as tumor biopsy samples cannot always be obtained, and because tumor heterogeneity can result in an incomplete set of neoantigens from a single biopsy, we developed ImmunoID NeXT circulating tumor DNA (ctDNA) Exome to (1) identify neoantigens in cell free DNA (cfDNA) as a complement to tumor biopsy derived neoantigens and (2) track neoantigens in the cfDNA post immuno-therapy treatment. To demonstrate the utility of the ImmunoID NeXT ctDNA Exome for both identification and monitoring of neoantigens directly from cfDNA, we have performed two extensive studies. Firstly, we obtained cfDNA from 2 healthy donors, mixed them to create somatic variants with AFs down to 0.5% with analytical sensitivity calculated against &amp;gt;10,000 variants. Secondly, we have performed extensive cfDNA testing in cancer patients to assess our capabilities across tumor types. Finally, and very importantly, we utilized multi-location primary and metastatic tumor profiling to demonstrate the ImmunoID NeXT cfDNA platform can be applied to profile tumor heterogeneity. Results: In our healthy donor mixes, we observed our ImmunoID NeXT cfDNA platform can detect de novo “gold set” SNVs with a sensitivity of 90% down to an allele frequency of 2%. For monitoring applications we are able to detect SNVs with a sensitivity of 92% down to an allele frequency of 0.5%. When tested across a range of tumor types including melanoma, lung, and colorectal, ImmunoID NeXT repeatedly detected high concordance for somatic events shared between tumor and cfDNA. In tumor samples allele frequencies ranged from10% to 100%, and through cfDNA interrogation 60%-98% of these events were accurately detected in the plasma. Finally, we were able to reproducibly detect ctDNA, which were not present in the primary tumor sample, in subsequent primary tumor biopsy curls or metastases in multiple tumor types, demonstrating our ctDNA platform can effectively monitor tumor heterogeneity. Conclusion: These results show the accuracy of the ImmunoID NeXT platform for detecting and profiling ctDNA somatic events. Further, these results demonstrate the potential of using a comprehensive ctDNA Exome to identify and monitor neoantigens as a complement to the results from sequencing of the tumor biopsy alone. Citation Format: Simo V. Zhang, Charles Abbott, Robin Li, Eric Levy, Shujun Luo, Robert Power, Rena McClory, John West, Richard Chen, Sean Michael Boyle. Development and validation of an accurate exome-scale cfDNA detection platform [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 4695.