Blood-Based Multi-Cancer Detection Using a Novel Variant Calling Assay (DEEPGEN(TM)): Early Clinical Results

SIMPLE SUMMARY: Cancer remains a worldwide concern with significant burdens on the population and healthcare systems. Studies have shown that early detection is paramount in positive patient outcomes, although the standard of care screening is limited to a few cancers. When a tumor cell dies, it releases DNA into the bloodstream. This cell-free DNA can be extracted, and specific mutations identified. Technologies based on this principle are gaining popularity amongst physicians for cancer patients to inform personalized treatment. Additionally, if platforms are sensitive enough, blood-based multi-cancer screening can be performed. DEEPGEN(TM) is a next-generation sequencing platform that has been optimized for early cancer detection. This study is a preliminary analysis of cancer detection rates across seven cancers using the DEEPGEN(TM) platform. ABSTRACT: This is an early clinical analysis of the DEEPGENTM platform for cancer detection. Newly diagnosed cancer patients and individuals with no known malignancy were included in a prospective open-label case-controlled study (NCT03517332). Plasma cfDNA that was extracted from peripheral blood was sequenced and data were processed using machine-learning algorithms to derive cancer prediction scores. A total of 260 cancer patients and 415 controls were included in the study. Overall, sensitivity for all cancers was 57% (95% CI: 52, 64) at 95% specificity, and 43% (95% CI: 37, 49) at 99% specificity. With 51% sensitivity and 95% specificity for all stage 1 cancers, the stage-specific sensitivities trended to improve with higher stages. Early results from this preliminary clinical, prospective evaluation of the DEEPGENTM liquid biopsy platform suggests the platform offers a clinically relevant ability to differentiate individuals with and without known cancer, even at early stages of cancer.