April 2024

In this research study, a multimodal epigenetic sequencing analysis (MESA) of cfDNA was introduced aiming to improve the non-invasive early detection of human cancers with deep targeted Enzymatic Methyl-seq (EM-seq).

Samples from 2 of 3 cohorts were collected in PAXgene Blood ccfDNA Tubes (RUO)* and cfDNA was extracted from plasma using the QIAGEN QIAsymphony DSP Circulating DNA Kit on the QIAsymphony SP instrument.

For the analysis of cfDNA the researchers (from University of California, Irvine, USA; Helio Genomics, Inc., USA; Soochow University, Suzhou, China) combined (1) cfDNA methylation, (2) nucleosome occupancy, (3) nucleosome fuzziness, and (4) window protection score (WPS) across gene promoters and polyadenylation sites. They could demonstrate that the introduction of novel modalities (e.g., nucleosome fuzziness) and genomic features (e.g., polyadenylation sites) improved cancer detection beyond traditional epigenetic markers (e.g., promoter DNA methylation). 

The results showed superior detection accuracy for colorectal, liver, and pancreatic cancers with MESA compared to single modality-models. Based on their findings, complementary epigenetic profiles of cfDNA could potentially be used for advanced non-invasive cancer detection.

Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection

Li, Y., Xu, J., Chen, C. et al. 

Genome Med 16, 9 (2024) https://doi.org/10.1186/s13073-023-01280-6

*The PAXgene Blood ccfDNA Tube is For Research Use Only. Not for use in diagnostic procedures.