Development of a pan-cancer DNA methylation biomarker

Authors

• N Jameel
• H Petrykowska
• G Margolin
• B Miller
• L Elnitski

Abstract

Every year, 1.6 million Americans are diagnosed with cancer. Although screening methods exist for a few cancer types, many tumors cannot be detected at early stages with current methods. Blood-based biomarkers that are effective at detecting the presence of tumor DNA from early stages are sought-after for their relatively low invasiveness. In a previous study, we have identified a putative DNA methylation biomarker located in the promoter region of the ZNF154 gene, which we found to be hypermethylated in 15 different solid tumor types relative to normal tissue. In this study, we tested the magnitude and pattern of differential methylation of a 302-bp region at ZNF154 using next generation sequencing of bisulfite converted DNA amplified from 184 tumor and 34 normal colon, lung, breast, stomach, and endometrial tissue samples. This sequencing technique allows for analysis of individual sequencing reads, which in turn allows for better discrimination between tumor and normal samples. Computational simulations of different concentrations of the tumor DNA diluted in normal DNA show that analysis of individual sequencing reads provides a more effective screening tool. Here, our preliminary data suggest that ZNF154 can be used to detect a tumor signal in cell-free DNA extracted from blood plasma samples. Starting with 1-2 mL of blood plasma we were able to detect highly methylated sequencing in significantly more samples from individuals with and without cancer. These data provide a proof of principle for the potential use of our previously identified biomarker for the tumor detection starting with patient blood samples.

Scientific Focus Area: Cancer Biology

This page was last updated on Friday, March 26, 2021