On-Chip Magnetic Extraction of Circulating Cell-Free DNA from Biological Samples

Methods Mol Biol. 2024:2804:65-75. doi: 10.1007/978-1-0716-3850-7_3.

Abstract

In recent years, the analysis of circulating cell-free DNA (cfDNA) containing tumor-derived DNA has emerged as a noninvasive means for cancer monitoring and personalized medicine. However, the isolation of cfDNA from peripheral blood has remained a challenge due to the low abundance and high fragmentation of these molecules. Here, we present a dynamic Magnetic ExTRactiOn (METRO) protocol using microfluidic fluidized bed technology to isolate circulating cfDNA from raw biological materials such as undiluted serum. This protocol maximizes the surface area for DNA binding within the chip in order to capture short DNA fragments. It uses only a few μL of sample and reagents. The protocol can be automated, and it is fully compatible with sensitive DNA amplification methods such as droplet-based digital PCR (ddPCR).

Keywords: Cancer; Circulating cell-free DNA; Circulating tumor DNA; Microfluidic fluidized bed; Solid-phase extraction.

MeSH terms

  • Cell-Free Nucleic Acids* / blood
  • Cell-Free Nucleic Acids* / genetics
  • Cell-Free Nucleic Acids* / isolation & purification
  • Humans
  • Lab-On-A-Chip Devices*
  • Magnetics / methods
  • Microfluidic Analytical Techniques / instrumentation
  • Microfluidic Analytical Techniques / methods
  • Neoplasms / blood
  • Neoplasms / diagnosis
  • Neoplasms / genetics
  • Polymerase Chain Reaction / methods