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

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. Clinicalintervention in the early stages of cancer can greatly improve the survival of cancerpatients. Despite the tremendous demand for early detection methods in the clinical practice, fewtechnologies exist on the market. To address this unmet need, with support from the NIH, ourpartner’s team at UCLA has developed an approach based on the genome-wide methylation analysis ofcell-free DNA (cfDNA). Their novel technology, called CancerDetector, not only detects cancer earlybut also infers its location (tissue of origin). To increase the power of thiscomputational framework, the same UCLA team together with EarlyDx team recently developeda novel experimental approach, called cell-free DNA Reduced Representation BisulfiteSequencing (cfRRBS), that efficiently enriches the cfDNA fragments covering methylationsites in a blood sample. Combining the two innovations yields a test with high sensitivity andspecificity in early-stage liver cancer patients. This test is now ready to be adapted for clinicaluse. The proposed project will translate these proof-of-principle laboratory protocols into acommercial-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 accurateand cost4effective genome4wide methylation profiling; Aim 2) Validate theEarlyDx4MethylScan assay for the detection of liver cancer. Engineered samples offragmented DNAs will be used in Aim 1 to ensure the reproducibility of the assayduring development. The CancerDetector algorithm has already been implemented in ourcloud-computing platform. Using this platform, the new assay will be used to perform cancerprediction in a cohort of 100 real liver cancer patients and 100 controls. Phase I will becompleted 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 commercializethe test: first as a research product for labs, and finally as a clinical product ready forhospitals.Cancer continues to be a major cause of mortality in the world, but currently no early screeningmethod has proven to be effective. The successful development and validation of the proposed cfDNAmethylome test will provide a new avenue for detecting and localizing cancer early. Commercializingthe proposed test will likely offer an important, noninvasive alternative to currentscreening modalities, such as low-dose CT in lung cancer, with a profound impact on cancerprevention.