2020 SITC: Profiling tumor circulating cell-free DNA with an enhanced whole-exome to enable sensitive assessment of somatic mutations

The analysis of tumors using circulating cell-free DNA (cfDNA) is beginning to transform cancer diagnosis, prognosis, response to therapy and to enable disease progression monitoring. Most cfDNA assays are centered around the identification of therapeutically actionable mutations and only cover a limited number of genes, and as such cannot inform on all genetic alterations present in the tumors. To address this, we have developed a whole-exome scale cfDNA platform, NeXT Liquid Biopsy™, that enables sensitive detection and tracking of mutations in approximately 20,000 genes. The NeXT LB platform generates comprehensive sequencing data derived from the cfDNA (plasma), the tumor (e.g. FFPE) and the patient’s germline (e.g. blood cells), and therefore enable to closely discover and monitor clonal and subclonal evolution of mutations in plasma, and novel genetic mutations following surgery, and/or treatment therapies.

To enable sensitive detection across the exome, we developed an enhanced exome assay and chemistry that augments hard to sequence genomic regions such as regions of high GC content, to enable more uniform coverage across the exome. Additionally, we achieve a high average depth of approximately 2000X for the entire exome, with additional boosted depth (5000X) for 247 clinically relevant oncogenic and tumor suppressor genes to further enhance sensitivity. For analysis, we developed a computational algorithm, Silencer, that enables accurate somatic mutation detection without compromising sensitivity in the plasma. Silencer is empowered by an error suppression model built from a panel of normal individual plasma samples, and custom filters including a dedicated blacklist that is tailored to our NeXT LB technology.