Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing

Genome Med. 2023 May 3;15(1):33. doi: 10.1186/s13073-023-01178-3.

Abstract

Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This approach generated up to 200 million reads for a single cfDNA sample from cancer patients, an order of magnitude improvement over existing nanopore sequencing methods. We developed a single-molecule classifier to determine whether individual reads originated from a tumor or immune cells. Leveraging methylomes of matched tumors and immune cells, we characterized cfDNA methylomes of cancer patients for longitudinal monitoring during treatment.

Keywords: Cell-free DNA; Methylation; Nanopore; Single-molecule sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell-Free Nucleic Acids* / genetics
  • DNA
  • DNA Methylation
  • Humans
  • Nanopore Sequencing*
  • Neoplasms* / genetics

Substances

  • Cell-Free Nucleic Acids
  • DNA