Enzymatic enrichment of unmethylated cell-free DNA improves the sensitivity of fragmentomic analysis for the diagnosis of patients with lung cancer

Global loss of genomic DNA methylation is associated with the progression of cancer. This genome-wide hypomethylation is thought to result from increased rates of genome replication in rapidly dividing cancer cells. We leveraged this aspect of cancer biology to address the challenge of early disease detection in cell-free DNA from a cohort of lung cancer patients. We combined Tagomics' Activace platform, which enriches unmethylated CpG sites of the genome for sequencing, with genome-wide, fragmentomic analysis on this hypomethylated DNA fraction. Using a single sample input (>5 ng of cell free DNA) Activace enables a multiomic (epigenomic and fragmentomic) read-out with only 70 M sequencing reads. We tested the utility of this approach on a small cohort of 36 patients, who presented at the clinic with symptoms of lung cancer, had a blood sample taken and went on to receive a diagnosis using gold-standard testing (imaging, pathology). The cohort contained 14 cancer-free patients, 12 patients with an early-stage (Stage I & II) diagnosis of non-small cell lung cancer and 10 patients with a late-stage (Stage III & IV) diagnosis of non-small cell lung cancer. We sequenced the cfDNA obtained from the plasma of these patients; and enriched and sequenced the unmethylated DNA fraction from the same patients, using Tagomics' Activace platform. We compared the fragmentomics profiles of both the enriched, unmethylated DNA and the whole cfDNA and evaluated the impact of the enrichment on our ability to classify the cohort. Using a leave-one-out approach, a logistic regression classifier, trained on the end motif profiles of the Activace dataset (enriched for unmethylated CpG sites), we correctly classified all but two of the early-stage lung cancer cases (91% sensitivity, 100% specificity). By contrast, using an analogous approach in the WGS dataset (whole cfDNA) eight lung cancer cases (seven early-stage and one late-stage) were misclassified (64% sensitivity, 100% specificity). Multiomics tools, such as the Tagomics' Activace platform enable information-rich insight into disease biology and will likely outperform single analyte-based tests, in the future. The enrichment of DNA containing unmethylated CpG sites improves sensitivity of fragmentomic analysis, relative to analogous analysis of the whole genome, likely due to the enrichment of tumour-derived, hypomethylated DNA fragments in patients with cancer.