SBIR-STTR Award

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.

Public Health Relevance Statement:
Cancer continues to be a major cause of mortality in the world, but currently no early screening method has proven to be effective. The successful development and validation of the proposed cfDNA methylome test will provide a new avenue for detecting and localizing cancer early. Commercializing the proposed test will likely offer an important, noninvasive alternative to current screening modalities, such as low-dose CT in lung cancer, with a profound impact on cancer prevention.

Project Terms:
Algorithms; Automation; Biological Assay; Assay; Bioassay; Biologic Assays; Blood; Blood Reticuloendothelial System; Malignant Neoplasms; Cancers; Malignant Tumor; malignancy; neoplasm/cancer; Cells; Cell Body; Decision Making; DNA; Deoxyribonucleic Acid; Engineering; Feasibility Studies; Future; Goals; Primary carcinoma of the liver cells; Hepatocarcinoma; Hepatocellular Carcinoma; Hepatocellular cancer; Hepatoma; Liver Cells Carcinoma; liver carcinoma; Hospitals; Laboratories; Libraries; Liver; hepatic body system; hepatic organ system; Liver Extract; liver transplantation; Hepatic Transplantation; Liver Grafting; Liver Transplant; Methods; Methylation; mortality; Names; United States National Institutes of Health; NIH; National Institutes of Health; Neoplasm Circulating Cells; circulating neoplastic cell; circulating tumor cell; Legal patent; Patents; Patients; Phenotype; Plasma; Blood Plasma; Plasma Serum; Reticuloendothelial System, Serum, Plasma; Research; medical schools; medical college; school of medicine; Sensitivity and Specificity; Technology; Testing; Time; Tissues; Body Tissues; Translating; base; Blood Sample; Blood specimen; improved; Procedures; Cancer Screening for Patients; early cancer detection; Screening for cancer; Site; Clinical; Phase; Ensure; Malignant Tumor of the Lung; Pulmonary Cancer; Pulmonary malignant Neoplasm; lung cancer; Malignant neoplasm of lung; cancer prevention; Hepatic Cancer; liver cancer; malignant liver tumor; Malignant neoplasm of liver; Nature; Complex; Protocol; Protocols documentation; Techniques; Location; Operative Procedures; Surgical; Surgical Interventions; Surgical Procedure; surgery; Operative Surgical Procedures; early detection; Early Diagnosis; cohort; novel; novel technologies; new technology; Modality; Reporting; early liver cancer detection; liver cancer detection; screening for liver cancer; Screening for Hepatocellular Cancer; Local Cancer; Localized Cancer; Localized Malignancy; Localized Malignant Neoplasm; Sampling; Intervention Strategies; interventional strategy; Intervention; Jasmine; Jasminum; Bio-Informatics; Bioinformatics; Effectiveness; Address; Data; Detection; Reproducibility; Cancer Control Science; Cancer Control; Cancer Detection; Cancer Patient; Senior Scientist; Validation; Preparation; Process; developmental; Development; cirrhotic; Cirrhosis; cost; computational framework; computer framework; computational tools; computerized tools; cost effective; cancer type; Hepatobiliary; innovate; innovative; innovation; multidisciplinary; user-friendly; computer algorithm; Computational algorithm; prototype; clinical practice; phase II study; phase 2 study; genomewide methylation; global methylation; genome wide methylation; screening; methylome; Cloud Infrastructure; cloud computer; Cloud Computing; cloud based; cell free circulating DNA; cell free DNA; methylation marker; methylation biomarker; BS-seq; Bisulfite-based sequencing; bisulfite-seq; bisulfite sequencing; CLIA accredited; CLIA approved; CLIA compliant; CLIA licensed; CLIA certified; cancer survival; liquid biopsy; early screening; computing platform; computational platform; low dose computerized tomography; low-dose CT; low dose computed tomography

The long-term goal of this SBIR Phase II project is to develop and market a commercially viable, blood-based methylation profiling test that can detect and locate multiple types of 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 clinical practice, few commercial tests exist in the market. To address this unmet need, in Phase I, we developed and validated a cell-free DNA Reduced Representation Bisulfite Sequencing assay, MethylScan assay, to interrogate the methylation profile of cfDNA. The MethylScan assay was highly reproducible and reliable at low input quantities of DNA and achieved high sensitivity and specificity for detecting liver cancer. DNA methylation is established during early mammalian cell differentiation and plays an important role in the development and progression of cancer; thus, it is an ideal biomarker not only for pan-cancer detection but also for identification of tumor tissue of origin. The proposed project will translate the MethylScan assay to a surveillance product for liver cancer and expand its intended use for early lung cancer detection in patients with indeterminate lung nodules. In this Phase II study, our specific aims are as follows: Aim 1) Optimize MethylScan assay and the workflow of MethylScan Test; Aim 2) Perform a clinical validation to evaluate MethylScan test for early detection of HCC; Aim 3) Perform a clinical validation to evaluate MethylScan test for early detection of lung cancer in patients with indeterminate lung nodules. The MethylScan test will be used to perform cancer prediction in a cohort of 200 early HCC patients, 70 early lung cancer patients with malignant lung nodules, 200 patients at high risk for HCC or 50 patients with benign lung nodules. Participants in the clinical validation study will be recruited from Midwest and West Coast sites. The outcome of this project will support large clinical trials for MethylScan test as a surveillance approach for patients at risk of liver and lung cancer. The data collected will be discussed with FDA in a pre-submission meeting.

Public Health Relevance Statement:
PROJECT NARRATIVE Cancer continues to be a major cause of mortality in the world, but current screening methods are suboptimal with limited sensitivity and/or specificity. The successful development and validation of the proposed cfDNA methylome test will provide a new avenue for detecting and localizing cancer early. Commercializing the proposed test will likely offer an important, more readily accessible blood-based alternative to current image- based screening modalities, such as ultrasound in liver cancer and low-dose CT in lung cancer, with a profound impact on cancer diagnosis and survival.

Project Terms:
Automation; Biological Assay; Assay; Bioassay; Biologic Assays; Biopsy; Blood; Blood Reticuloendothelial System; Malignant Neoplasms; Cancers; Malignant Tumor; malignancy; neoplasm/cancer; Case-Control Studies; Case-Base Studies; Case-Comparison Studies; Case-Compeer Studies; Case-Referent Studies; Case-Referrent Studies; case-controlled studies; Cell Differentiation process; Cell Differentiation; Clinical Research; Clinical Study; Clinical Trials; Complement; Complement Proteins; Data Analyses; Data Analysis; data interpretation; DNA; Deoxyribonucleic Acid; Future; Goals; Gold; Primary carcinoma of the liver cells; Hepatocarcinoma; Hepatocellular Carcinoma; Hepatocellular cancer; Hepatoma; Liver Cells Carcinoma; liver carcinoma; Laboratories; Lead; Pb element; heavy metal Pb; heavy metal lead; Libraries; Lung; Lung Respiratory System; pulmonary; Magnetic Resonance Imaging; MR Imaging; MR Tomography; MRI; MRIs; Medical Imaging, Magnetic Resonance / Nuclear Magnetic Resonance; NMR Imaging; NMR Tomography; Nuclear Magnetic Resonance Imaging; Zeugmatography; Medicine; Methods; Methylation; Michigan; Midwestern United States; Midwest; Midwest U.S.; Midwest US; mortality; Names; Metastasis; Metastasize; Metastatic Lesion; Metastatic Mass; Metastatic Neoplasm; Metastatic Tumor; Secondary Neoplasm; Secondary Tumor; cancer metastasis; tumor cell metastasis; Neoplasm Metastasis; Nodule; Patients; Play; Prospective Studies; pulmonary nodule; Lung nodule; General Radiology; Radiology; Radiology Specialty; Research; Risk; social role; Role; Sensitivity and Specificity; Specificity; Technology; Testing; Time; Tissues; Body Tissues; Translating; Universities; Hepatology; base; tumor progression; cancer progression; neoplasm progression; neoplastic progression; Blood specimen; Blood Sample; improved; Screening for cancer; Cancer Screening for Patients; early cancer detection; Site; Benign; Clinical; Malignant - descriptor; Malignant; Phase; Histologic; Histologically; Lesion; Malignant Tumor of the Lung; Pulmonary Cancer; Pulmonary malignant Neoplasm; lung cancer; Malignant neoplasm of lung; lung cancer early detection; lung cancer screening; Hepatic Cancer; liver cancer; liver malignancy; malignant liver tumor; Malignant neoplasm of liver; DNA Methylation; Tumor Tissue; Operative Procedures; Surgical; Surgical Interventions; Surgical Procedure; surgery; Operative Surgical Procedures; meetings; early detection; Early Diagnosis; Performance; professor; cohort; Participant; validation studies; Modality; Devices; early liver cancer detection; liver cancer detection; screening for liver cancer; Screening for Hepatocellular Cancer; Local Cancer; Localized Cancer; Localized Malignancy; Localized Malignant Neoplasm; Sampling; Intervention Strategies; interventional strategy; Intervention; cancer diagnosis; Bio-Informatics; Bioinformatics; Oncogenesis; tumorigenesis; AFP; FETA; HPAFP; AFP gene; Address; Data; Detection; Mammalian Cell; Reproducibility; TNM staging system; TNM; American College of Radiology Imaging Network; ACRIN; Cancer Detection; Cancer Patient; Small Business Innovation Research Grant; SBIR; Small Business Innovation Research; Validation; Process; Development; developmental; Cirrhosis; cirrhotic; Image; imaging; Outcome; cost effective; cancer type; prospective; multidisciplinary; prototype; commercialization; high risk; molecular marker; molecular biomarker; Biological Markers; bio-markers; biologic marker; biomarker; clinical practice; phase 2 study; phase II study; screening; methylome; Big Data; BigData; cell free DNA; cell free circulating DNA; bisulfite sequencing; BS-seq; Bisulfite-based sequencing; bisulfite-seq; imaging biomarker; imaging marker; imaging-based biological marker; imaging-based biomarker; imaging-based marker; CLIA certified; CLIA accredited; CLIA approved; CLIA compliant; CLIA licensed; cancer survival; liquid biopsy; recruit; machine learning algorithm; machine learned algorithm; machine learning based algorithm; low dose computed tomography; low dose computerized tomography; low-dose CT; detection method; detection procedure; detection technique; machine learning classifier; machine learning based classifier; ultrasound