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.
Related
- Comparative outcomes of natural orifice specimen extraction surgery versus conventional minilaparotomy-assisted specimen extraction in colorectal cancer: A single-center retrospective study.
- Application of a Quantitative POCT-FIT Based on Near-Infrared Fluorescence Immunochromatography in Population-Based Colorectal Cancer Screening: A Comparative Evaluation with a Centralized Testing System
- Comparative Evaluation of Microwave- and Ultrasound-Assisted Extraction of Antioxidants from Parsley (Petroselinum crispum (Mill.) Fuss) and Coriander (Coriandrum sativum L.) Processing By-Products.
- Comparative evaluation of large language models for guideline-concordant decision support in colorectal cancer multidisciplinary team care: A source-masked retrospective study
- Environmental impact of urine analyses: Comparison of manual, semi and fully automated analytical workflows
BibTeX
@article{denninghoff2026comparative,
title = {{Comparative evaluation of two automated magnetic-bead cfDNA extraction workflows in early colorectal cancer}},
author = {Valeria Denninghoff and Inés Aznar-Peralta and Cristóbal Fresno and Álvaro Mellado-Cuesta and Simona Innamorato and María Pilar Molina-Vallejos and Javier López-Hidalgo and María José Serrano},
journal = {Scientific Reports},
year = {2026},
month = oct,
doi = {10.1038/s41598-026-69239-2},
url = {https://www.nature.com/articles/s41598-026-69239-2},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Comparative evaluation of two automated magnetic-bead cfDNA extraction workflows in early colorectal cancer
AU - Valeria Denninghoff
AU - Inés Aznar-Peralta
AU - Cristóbal Fresno
AU - Álvaro Mellado-Cuesta
AU - Simona Innamorato
AU - María Pilar Molina-Vallejos
AU - Javier López-Hidalgo
AU - María José Serrano
PY - 2026
DA - 2026/10/27
JO - Scientific Reports
DO - 10.1038/s41598-026-69239-2
UR - https://www.nature.com/articles/s41598-026-69239-2
AB - 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.
SN - 2045-2322
ER -