Helio Genomics, the creator of the HelioLiver test, recently evaluated its multimodal epigenetic sequencing assay (MESA) for colon cancer detection. Their findings suggest that combining cell-free DNA (cfDNA) methylation features and cfDNA fragmentomics-derived features can improve the ability to identify patients who have colon cancer. 

Harnessing cfDNA for Colon Cancer Detection

In the past decade, alterations in cfDNA methylation patterns have gained wide acceptance as powerful biomarkers for early cancer detection. Helio Genomics specializes in studying and incorporating these biomarkers into their own products.

The company evaluated MESA for colon cancer detection, which combines cfDNA methylation with features derived from cfDNA fragmentomics, such as nucleosome occupancy, to improve diagnostic performance. 

Their study indicated that MESAs combined approach is superior at distinguishing between colon cancer patients and healthy individuals compared to methods that use just cfDNA methylation alone or cfDNA fragmentomics alone.

Colon Cancer Study

To conduct this study, blood specimens drawn from 64 subjects with colon cancer and 67 subjects without cancer (as control) were processed using Helio Genomics advanced wet-lab platform, ECLIPSE, which consists of molecular techniques for cfDNA extraction, conversion, library generation, and targeted next-generation sequencing (NGS).

Custom bioinformatics pipelines and algorithms were then used to process sequencing data, generate features, and train models.

The Helio Genomics study indicates that cfDNA fragmentomics-derived features may carry complementary and additive information to the cfDNA methylation signal. By utilizing improved molecular techniques and analysis methods, it is possible for Helio Genomics to evaluate both cfDNA methylation and cfDNA fragmentomics features that reflect the underlying DNA chromatin structure within a single assay. 

“Most cfDNA methylation sequencing-based tests are unidimensional in their approach, focusing on methylation patterns alone,” says Shivani Mahajan, director of Computational Biology at Helio Genomics. “As a result, they fail to capture the vast depth of epigenetic information present in the cfDNA fragments. Our multimodal approach provides us with a more complete picture of the epigenetic landscape of cancer and enhances our ability to detect cancer early, when curative treatment is possible.”

The company says this newly founded multimodal approach will allow for the development of diagnostic tests with superior performance characteristics compared to current testing methods.