Development and validation of an accurate exome-scale cfDNA detection platform

Neoantigens are increasingly used as biomarkers for 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 a matched normal sample to enable identification of putative neoantigens, which occur across the genome. 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 our ImmunoID NeXT cfDNA platform. Our aim was two-fold: (1) to identify neoantigens in cell free DNA (cfDNA) as a complement to tumor biopsy derived neoantigens and, (2) to track neoantigens in the cfDNA post immuno-therapy treatment. In contrast to most current tumor cfDNA tests, which are designed to assess a small number of variants or genes (often <100), our ACE ctDNA Exome platform covers ~ 20,000 genes at very high sequencing depth to accurately identify lower allele frequency variants, allowing for the detection of many putative neoantigens that could be missed when employing targeted approaches. In the present study, we assess the limit of detection (LOD) of our ImmunoID NeXT cfDNA platform assay for small nucleotide variants (SNVs) and demonstrate the utility of the assay for both monitoring and de novo identification of neoantigens directly from cfDNA.