Exploiting signals of cell-free DNA degradation for clinical research and cancer diagnostics - Summary
Claret Bioscience is developing a next-generation sequencing (NGS) library preparation
technique that can be deployed as a liquid biopsy DNA assay. Liquid biopsy recovers biomarkers like
DNA and other cellular material found circulating in the blood and other bodily fluids, called cell-free
DNA (cfDNA). In individuals with tumors, a small portion of the overall cfDNA will derive from the
cancerous cells, sharing somatic variants with the tumor itself. Liquid biopsy thus promises a non-
invasive means of detecting and genotyping a patient's solid tumor. However, there are few cfDNA-
based assays approved today for clinical diagnostic use. They are restricted to relatively few known
cancer-driving variants, limiting the scope of cancer screening and the utility of high-throughput
sequencers.
Claret's solution is an NGS liquid biopsy assay that aims to broadly and agnostically identify
DNA of abnormal origin. Our high-throughput assay exploits a novel cfDNA biomarker by recovering
and charactering signals of DNA degradation found only at the termini of cfDNA fragments. The major
potential outcome of our technology is a liquid biopsy tool that is additive, providing valuable cfDNA
sequence data while simultaneously exploiting biologically degraded fragment ends - information lost to
all NGS methods to date.
The technical challenge of bringing our innovation to the NGS and/or liquid biopsy market
hinges on two central challenges. First, the assay must efficiently convert a pool of cfDNA molecules
into a sequencing library with high fidelity such that the actual DNA molecular ends are captured. Our
first Phase I goal is thus assay optimization. We will measure fidelity, efficiency, reproducibility,
sensitivity using a series of experimentally-designed synthetic controls. The second challenge is to
discern the biological utility of the characterization of cfDNA termini. We designed our second aim of
Phase I to probe for specific signals that may be indicative of disease state and assayable from cfDNA.
We focus on matched sets (tissue diseased, tissue normal, blood plasma) of clinical samples from
treatment-naïve donors with known cancer types. The proposed Phase I proof-of-concept experiments
and assay optimizations will yield a path to a commercially viable product capable of revealing
important patterns of DNA degradation from healthy and diseased samples.
Project Summary - 1
