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

> **NIH NIH R43** · EARLYDIAGNOSTICS, INC. · 2020 · $351,646

## Abstract

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.

## Key facts

- **NIH application ID:** 10009786
- **Project number:** 1R43CA246941-01A1
- **Recipient organization:** EARLYDIAGNOSTICS, INC.
- **Principal Investigator:** Xiaohui Ni
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $351,646
- **Award type:** 1
- **Project period:** 2020-06-01 → 2021-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10009786

## Citation

> US National Institutes of Health, RePORTER application 10009786, An Accurate, Non-invasive, and Cost-effective Methylome Test for Early Cancer Detection (1R43CA246941-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10009786. Licensed CC0.

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