Circulating cell-free DNA

High yields with chemagic automated or manual purification of circulating cell free DNA

Circulating cell free DNA (cfDNA) in body fluids is being used for non-invasive, real-time biomarker research and more. Yet detection is often challenged by its low levels, fragmentation and preanalytical variabilities introduced by sample collection, plasma preparation, and nucleic acid purification.

Revvity chemagic cfDNA isolation kits, together with dedicated chemagic instruments rely on patented chemagic technology using M-PVA Magnetic beads to ensure a high quality of nucleic acid purification. Comparable yields to manual spin column methods were obtained with efficient removal of contaminants and exclusion of cross-contamination. With automation, variabilities associated with multiple handling steps are reduced and sample integrity maintained with full sample tracking capabilities.

Benefits of automated cfDNA isolation with chemagic™ technology:

• Reliable and comparable yields to manual methods
• Fast, automated workflow with on-board lysis and no heating required
• Wide range of sample inputs applicable from 0.5 to 18 ml
• Full sample tracking with barcode reading and bidirectional LIMS communication capability
• Ability to isolate viral nucleic acids
• Suitable for fresh or frozen plasma/serum from EDTA, citrate or Streck® Cell-free DNA BCT® tubes
• Downstream compatibility with various assays - ddPCR, NGS, qPCR etc.
• Compatibility with other automated Revvity systems

Customer review

“The chemagic™ cfDNA extraction kit on the chemagic 360 platform has greatly reduced the hands-on time needed for sample preparation. It has also given us improved cfDNA yields compared to the current, manual approach used in our laboratory and enabled significantly higher throughput. The ease-of-use of the system is high and has made it easy for us to rapidly train our staff and implement the approach in our day-to-day practice.”
Veli-Mikko Puupponen, CEO, BiopSense Oy/Ltd, Finland

“We use cfDNA extracted with chemagic™ technology in digital droplet PCR (ddPCR) assays to support diagnosis of colorectal cancer (Calleson et al., 2022), lung cancer (Frank et al., 2022) and anal cancer (based on HPV cfDNA detection, Lefèvre et al., 2021) with a sample to result turnaround time of 48 h.”
Professor Niels Pallisgaard, Dept of Pathology, Zealand University Hospital, Denmark

References:

1. Kwon, HJ., Shin, S.H., Kim, H.H. et al. Advances in methylation analysis of liquid biopsy in early cancer detection of colorectal and lung cancer. Sci Rep 13, 13502 (2023).
2. Frank, M. S., Andersen, C. S. A., Ahlborn, L. B., Pallisgaard, N., Bodtger, U., & Gehl, J. Circulating Tumor DNA Monitoring Reveals Molecular Progression before Radiologic Progression in a Real-life Cohort of Patients with Advanced Non–small Cell Lung Cancer. Cancer Research Communications, 2022; 2(10), 1174–1187.
3. Callesen LB, Hansen TF, Andersen RF, Pallisgaard N, Kramer S, Schlander S, Rafaelsen SR, Boysen AK, Jensen LH, Jakobsen A, Spindler KG. OPTIMISE: Optimisation of treatment selection and follow-up in oligometastatic colorectal cancer - a ctDNA-guided phase II randomised approach. Study protocol. Acta Oncol. 2022 Sep;61(9):1152-1156.
4. Kirchweger P, Kupferthaler A, Burghofer J, Webersinke G, Jukic E, Schwendinger S, Wundsam H, Biebl M, Petzer A, Rumpold H. Prediction of response to systemic treatment by kinetics of circulating tumor DNA in metastatic pancreatic cancer. Front Oncol. 2022 Aug 30;12:902177.
5. Kirchweger P, Kupferthaler A, Burghofer J, Webersinke G, Jukic E, Schwendinger S, Weitzendorfer M, Petzer A, Függer R, Rumpold H, Wundsam H. Circulating tumor DNA correlates with tumor burden and predicts outcome in pancreatic cancer irrespective of tumor stage. Eur J Surg Oncol. 2022 May;48(5):1046-1053.
6. Broholm M, Bojesen R, Gögenur M, Weinberger Rosen A, Watt S, Bulut M, Vogelsang R, Quist Jensen H, Orhan A, Bjerrum E, Søs Auður Andersen C, Pallisgaard N, Litman T, Troelsen JT, Gögenur I. Circulating Cell-Free DNA and Systemic Inflammatory Response after Self-Expandable Metal Stent for Malignant Bowel Obstruction. Archives of Microbiology and Immunology 6 (2022): 247-255.
7. Lefèvre AC, Pallisgaard N, Kronborg C, Wind KL, Krag SRP, Spindler KG. The Clinical Value of Measuring Circulating HPV DNA during Chemo-Radiotherapy in Squamous Cell Carcinoma of the Anus. Cancers (Basel). 2021 May 18;13(10):2451.
8. Yu J, Cho E, Choi J, Lim JE, Lee J, Kang M, Sung HH, Jeong BC, Seo SI, Jeon SS, Lee HM, Jeon HG. Genomic mutation profiling using liquid biopsy in Korean patients with prostate cancer: Circulating tumor DNA mutation predicts the development of castration resistance. Investig Clin Urol. 2021 Mar;62(2):224-232.
9. Moon SM, Kim JH, Kim SK, Kim S, Kwon HJ, Bae JS, Lee S, Lee HS, Choi MY, Jeon BH, Jeong BH, Lee K, Kim HK, Kim J, Um SW. Clinical Utility of Combined Circulating Tumor Cell and Circulating Tumor DNA Assays for Diagnosis of Primary Lung Cancer. Anticancer Res. 2020 Jun;40(6):3435-3444.