NCM 2023 Houston: Nanopore sequencing of cell-free DNA for methylation-based breast cancer detection

Liquid biopsies are increasingly being used as a cancer detection modality. Epigenetic characterization of cell-free DNA (cfDNA), specifically DNA methylation, is an emerging approach for sensitive detection and quantification of tumor burden. Detection of early-stage cancers remains an ongoing challenge due to lower amounts of tumor-specific DNA molecules found in cfDNA. In the context of breast cancer detection, existing cfDNA analysis methods suffer from poor sensitivity especially at earlier stages of malignancy. Solving this challenge, we developed a novel approach for single-molecule methylation analysis of cfDNA from cancer patients. Our study consists of a large cohort (~200 with stage I-II breast cancer and ~400 healthy controls). We successfully distinguished breast cancer cfDNA samples from healthy controls based on separate validation datasets. Overall, our study demonstrates that our nanopore-based cfDNA sequencing method can be an effective and scalable method for the non-invasive detection of breast cancer from blood.