Cost-effective DNA methylation-based assay for detecting early-stage cancers

October 2022 Cancer trials Nalinee Pandey

Researchers have developed a cost-effective method of detecting cell-free DNA methylation signatures for the early detection of cancers. This study was recently published in the reputed journal Nature Communications.

Alteration in DNA methylation is commonly observed across tumour types. Detecting these epigenetic changes using cell-free DNA can be an excellent diagnostic tool. However, this approach has a crucial bottleneck issue due to lower blood tumour fragment levels and molecular heterogeneity among solid tumours. Professor Zhou and colleagues from the University of California, Los Angeles, have developed a cost-effective method of capturing a high number of tumour fragments. Here, they perform a methylation-sequencing of cell-free tumour DNA fragments and computationally extract DNA-methylation-based signatures for detecting cancers.

Study Design

The researchers have tested the diagnostic potency of their method (cell-free DNA methylome sequencing) in a group of cancer patients. The test involved 217 samples from cancer patients {colon (n = 49), liver (n = 30), lung (n = 106) or stomach cancer (n = 32) and 191 samples as controls. The experimental assay and computational analysis were performed to assess the efficacy of the diagnostic method.

Main Findings

The diagnostic assay had a sensitivity of 74.5% (95% CI, 54.1-87.7) in detecting stage I and II disease. Overall, the method has an 80.7% accuracy for detecting all-stage cancers, which was increased (89.1%) for locating tissue of origin for all-stage cancers. The assay also has a high sensitivity of 85% for finding tissue-of-origin for early-stage cancer.


Cell-free DNA methylation assay is highly accurate and cost-effective for detecting cancers early. According to Prof. Zhou, “We are storing all the information we gather on our patients, so as our sample size increases, it may help us detect new biomarkers that can help detect and diagnose disease in the future.”


Stackpole, M.L., Zeng, W., Li, S. et al. Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. Nat Commun 13, 5566 (2022).