An Accurate, Non-invasive, and Cost-effective Methylome Test for Early Cancer Detection

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The long-term goal of this project is to develop and market a commercially viable, blood-based methylation profiling test that can detect and locate cancer early. Clinical intervention in the early stages of cancer can greatly improve the survival of cancer patients. Despite the tremendous demand for early detection methods in the clinical practice, few technologies exist on the market. To address this unmet need, with support from the NIH, our partner’s team at UCLA has developed an approach based on the genome-wide methylation analysis of cell-free DNA (cfDNA). Their novel technology, called CancerDetector, not only detects cancer early but also infers its location (tissue of origin). To increase the power of this computational framework, the same UCLA team together with EarlyDx team recently developed a novel experimental approach, called cell-free DNA Reduced Representation Bisulfite Sequencing (cfRRBS), that efficiently enriches the cfDNA fragments covering methylation sites in a blood sample. Combining the two innovations yields a test with high sensitivity and specificity in early-stage liver cancer patients. This test is now ready to be adapted for clinical use. The proposed project will translate these proof-of-principle laboratory protocols into a commercial-grade assay, and validate its effectiveness for the detection of liver cancer. This project is for a Phase I feasibility study. Our specific aims are as follows: Aim 1) Develop a commercial prototype of the EarlyDx4MethylScan assay for accurate and cost4effective genome4wide methylation profiling; Aim 2) Validate the EarlyDx4MethylScan assay for the detection of liver cancer. Engineered samples of fragmented DNAs will be used in Aim 1 to ensure the reproducibility of the assay during development. The CancerDetector algorithm has already been implemented in our cloud-computing platform. Using this platform, the new assay will be used to perform cancer prediction in a cohort of 100 real liver cancer patients and 100 controls. Phase I will be completed by successfully demonstrating the feasibility of liver cancer early detection. Phase II (and beyond) will further apply the test to multiple types of cancer, and eventually commercialize the test: first as a research product for labs, and finally as a clinical product ready for hospitals.