A high-throughput protocol for isolating cell-free circulating tumor DNA from peripheral blood

Area of Science:

• Molecular Biology
• Oncology
• Biotechnology

Background:

• Analysis of cell-free circulating tumor DNA (ctDNA) offers a less invasive method for monitoring cancer progression and treatment response compared to traditional tumor biopsies.
• Current ctDNA isolation methods rely on plasma separation via centrifugation, a process that is time-consuming and hinders automation.

Purpose of the Study:

• To develop and validate an automatable magnetic bead-based method for ctDNA isolation directly from peripheral blood (PB).
• To eliminate the centrifugation step required in standard plasma-based ctDNA isolation protocols.

Main Methods:

• A novel magnetic bead-based protocol was designed for ctDNA purification directly from peripheral blood.
• ctDNA was isolated from both peripheral blood and plasma samples of cancer patients using the developed method and standard protocols for comparison.

Main Results:

• The magnetic bead-based method successfully purified ctDNA directly from peripheral blood, bypassing the need for centrifugation.
• Allelic fractions of somatic single-nucleotide variants detected in target gene capture libraries were comparable between ctDNA isolated from PB and plasma.

Conclusions:

• The developed automatable magnetic bead-based method provides a viable alternative to plasma-based ctDNA isolation.
• This peripheral blood-based approach may replace current plasma protocols, offering a more efficient and automatable solution for cancer monitoring.