Best practices in cfDNA purification
Discover here tips and tricks for optimizing your cfDNA extraction process, enabling maximum yield and purity while minimizing contamination and degradation. Whether you're new to cfDNA extraction or looking to refine your existing protocols, these strategies will help you overcome common obstacles and achieve more consistent, reliable results.
Discover here tips and tricks for optimizing your cfDNA extraction process, enabling maximum yield and purity while minimizing contamination and degradation. Whether you're new to cfDNA extraction or looking to refine your existing protocols, these strategies will help you overcome common obstacles and achieve more consistent, reliable results.
Protocol for cfDNA isolation from cerebrospinal fluid
Current approaches for isolating cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) lack standardization, creating challenges for clinical research applications. To address this gap, a customer developed an optimized cfDNA isolation protocol specifically designed for CSF specimens.
Current approaches for isolating cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) lack standardization, creating challenges for clinical research applications. To address this gap, a customer developed an optimized cfDNA isolation protocol specifically designed for CSF specimens.
ctDNA reference standards
Mimix™ reference standards are cell line-derived to closely mimic patient samples. For over a decade, Revvity has been producing reference standards in the format of ctDNA for the surveillance of minimal residual disease (MRD) tracked via liquid biopsy. Our reference standards are available with matched negative controls to suit assay requirements.
Mimix™ reference standards are cell line-derived to closely mimic patient samples. For over a decade, Revvity has been producing reference standards in the format of ctDNA for the surveillance of minimal residual disease (MRD) tracked via liquid biopsy. Our reference standards are available with matched negative controls to suit assay requirements.
Advancing cancer research through epigenetic profiling
A groundbreaking study published in Communications Medicine demonstrates how distinguishing 5-methylcytosine (5mC) from 5-hydroxymethylcytosine (5hmC) in cell-free DNA dramatically enhances early colorectal cancer finding.
The study utilized the chemagic™ cfDNA 5k Kit which enabled high-quality cfDNA extraction from just 1-7 mL of plasma while preserving the epigenetic marks. This was needed for reliable base-resolution methylation profiling using 6-base sequencing chemistry.
A groundbreaking study published in Communications Medicine demonstrates how distinguishing 5-methylcytosine (5mC) from 5-hydroxymethylcytosine (5hmC) in cell-free DNA dramatically enhances early colorectal cancer finding.
The study utilized the chemagic™ cfDNA 5k Kit which enabled high-quality cfDNA extraction from just 1-7 mL of plasma while preserving the epigenetic marks. This was needed for reliable base-resolution methylation profiling using 6-base sequencing chemistry.
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
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References:
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Song, Ho Hyun et al. “Optimization of a Protocol for Isolating Cell-free DNA From Cerebrospinal Fluid.” Annals of laboratory medicine vol. 44,3 (2024): 294-298.
- Puddu, F., Johansson, A., Modat, A. et al. 5-methylcytosine and 5-hydroxymethylcytosine are synergistic biomarkers for early detection of colorectal cancer. Commun Med 6, 15 (2026).
