The Multimodal Epigenetic Sequencing Assay (MESA) from Helio Genomics has been evaluated to find that combining cell-free DNA (cfDNA) methylation features and cfDNA fragmentomics-derived features, such as nucleosome occupancy, can improve the ability to identify patients who have colon cancer. This 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, Helio Genomics can evaluate both cfDNA methylation and cfDNA fragmentomics features that reflect the underlying DNA chromatin structure within a single assay.