Comparative evaluation of two automated magnetic-bead cfDNA extraction workflows in early colorectal cancer

Abstract Reliable plasma cell-free DNA extraction is a key component of liquid biopsy testing and requires standardized preanalytical workflows. We conducted a paired comparison of 2 automated extraction methods, the Maxwell RSC ccfDNA LV Plasma Kit and the Maxwell RSC Rapid ccfDNA Kit, using EDTA plasma samples from 48 patients with early-stage colorectal cancer. For each patient, 4 mL of plasma was divided into two 2 mL aliquots and processed on the same instrument according to the manufacturer’s instructions. Cell-free DNA was measured by fluorometry and capillary electrophoresis, and outcomes were analyzed using linear mixed-effects models with extraction kit as a fixed effect and patient as a random intercept. Measurements obtained by the two analytical platforms were strongly correlated. Compared with the Standard workflow, the Rapid workflow showed significantly higher values across all evaluated concentration and fragment-distribution endpoints, including total DNA concentration and fragment recovery in the 50–700 bp and 100–300 bp ranges. In this early-stage colorectal cancer cohort, the Rapid workflow showed higher cfDNA recovery and a greater representation of fragments within the evaluated cfDNA size ranges than the Standard workflow. These findings are limited to upstream extraction and quality-control metrics and do not establish improved mutation detection, analytical sensitivity, or suitability for downstream molecular assays. The findings indicate that this simplified workflow may be a practical alternative for routine plasma cell-free DNA extraction, although local analytical verification remains advisable.