Cell-Free DNA (cfDNA) and FFPE Extraction
for Cancer Research

Cell-free DNA (cfDNA) refers to fragments of DNA that are found circulating freely in the bloodstream or other bodily fluids. Types of cfDNA include circulating tumor DNA (ctDNA), cell-free fetal DNA (cffDNA), cell-free mitochondrial DNA (ccf mtDNA), and donor-derived cell-free DNA (dd-cfDNA).

Efficient nucleic acid isolation that specifically recovers the circulating genetic material containing information related to the disease state is the first step in attaining valuable information. The importance of cfDNA is becoming established, but it may not tell the whole story. Cell-free RNA (cfRNA) sequences may serve as biomarkers as well in the form of microRNAs and gene fusions. Inclusion of cfRNA with cfDNA research provides an opportunity for researchers to expand their studies and advance human health.

Formalin-fixed paraffin-embedded (FFPE) tissue samples have proven vital to advancing cancer research. FFPE samples allow for a fuller analysis of precious samples, including investigation of important biomarkers, such as hotspot mutations, CNVs, gene fusions, and indels.

Discover end-to-end workflow solutions for your cancer research

Speed up your deparaffinization process with the Applied Biosystems AutoLys system. Comprised of pretreated tubes and a rack system to reduce pipetting steps, the system eliminates the need for hazardous chemicals and minimizes loss of tissue sample.

Explore: AutoLys products

Use our cell-free total nucleic acid (cfTNA) kit or cfDNA kit with KingFisher instruments and Oncomine assays to optimize the liquid biopsy workflow from extraction and purification to analysis.

Beads bind the DNA more efficiently than glass fiber filters, resulting in higher and more consistent yields. Additionally, because filters and vacuum manifolds are not used, there is no risk of cellular particulates clogging these items during the extraction process. This clogging issue is of particular concern with protein-rich, large-volume samples such as plasma that are commonly used in cfDNA studies.

MagMAX kits leverage Dynabeads technology for sample extraction, one of the leading magnetic beads in the industry. The Dynabeads MyOne Silane beads contained in the MagMAX Cell-Free Isolation kits have an optimized silica-like surface chemistry with high specific surface area that allows efficient kinetics and high sensitivity in nucleic acid capture. These aspects make Dynabeads MyOne Silane ideal for the recovery of circulating cell-free nucleic acid targets present at low concentrations in cell-free body fluids or FFPE. Once captured, these fragments can then be eluted in small elution volumes of 15 µL to 50 µL and are ready for downstream applications.

Learn more: Protocols for cell free cfDNA, cfTNA, and FFPE extractions