What’s cfDNA? What’s ctDNA?
Cell free DNA (cfDNA) refers to DNA fragments that is freely circulating in the bloodstream. cfDNA fragments have been thought to be continuously released into the circulation following apoptosis and necrosis of both cancerous and noncancerous cells, considering that they have the same sizes as the nucleosome unit. When cfDNA is released by cancer cells, it is specifically known as circulating tumor DNA (ctDNA). Previous studies have suggested that ctDNA can reflect tumor burden and guide potential therapeutic targets.
Why are cfDNA & ctDNA so important?
New liquid biopsy testing technology utilizing cfDNA as circulating biomarkers has been applied in clinical medicine with multiple FDA approved test on market, for example, detection of epithelial growth factor receptor (EGFR) mutations with ctDNA in non-small cell lung cancer (NSCLC) has been approved as a companion diagnostic for EGFR tyrosine kinase inhibitors (EGFR-TKIs). Despite burgeoning research and clinical application development activities using cfDNA, the origin of ctDNA has not yet been precisely established. A recent report demonstrated bimodal peaks of long fragment circulating cfDNA of 5 kb and short fragment cfDNA of 170 bp in patients with advanced lung cancer, and both contained ctDNA. It is also reported that selecting cfDNA fragments between 90-150 bp improved detection of tumor DNA. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alternations that were otherwise not detected.
How to perform cfDNA extraction?
Figure 1. MagVigen™ cfDNA Extraction workflow.
- Lyse: Lyse plasma sample.
- Bind: Mix MagVigen™ nanoparticles with sample. Nanoparticles bind to the cfDNA fragments.
- Wash 1: The beads respond to a magnetic force (by use of a magnet, e.g. magnetic separation rack), allowing bound material to be rapidly and efficiently separated from the rest of the sample. Remove unbound materials by aspiration, what remains is the nanoparticle-bound targets.
- Elute: Release the bound target size fragments from the nanoparticle.
- Bind 2: Mix MagVigen™ nanoparticles with sample. Nanoparticles bind to the cfDNA fragments.
- Wash 2/3: Remove unbound materials by aspiration, what remains is the nanoparticle-bound targets.
- Elute 2: Release the bound target size fragments from the nanoparticle. The selected DNA/RNA sample is ready for downstream applications.
How can we help?
MagVigen does cfDNA extraction and DNA sizing and cleanup
These and many other studies strongly support the necessity of continuous improvement and refinement of cfDNA extraction and DNA fragment size selection to enhance our understanding of this important type of circulating biomarkers, and better develop ctDNA clinical testing assays for cancer treatment monitoring and guidance or earlier detection. At NVIGEN, we are dedicated to developing highly sensitive sample and assay technology to empower personalized medicine. Our cfDNA extraction product and DNA sizing and cleanup nanobeads are popular choices to achieve high yield and high quality cell free DNA and discrete clean DNA fragment size ranges for a wide range of downstream genome-wide or targeted sequencing workflow. Customized product and assay development requests can be addressed to email@example.com to increase the potential applications of cfDNA and ctDNA for discovery research of tumor biology, clinical diagnostics, earlier cancer detection and targeted cancer therapy.