cfDNA vs. ctDNA
cfDNA (cell-free DNA) refers to DNA fragments that are no longer confined or encapsulated in a cell, and instead, 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 both have the same sizes (170bp) as the nucleosome unit.
cfDNA circulates in both healthy and pathological conditions. In addition to presenting bloodstream, i.e. in plasma and serum, it also presents in cerebral spinal fluid and saliva. cfDNA used to be a great target for Non-Invasive Prenatal Testing (NIPT) to screen for certain chromosomal disorders, e.g. Down syndrome. It’s now more and more used in liquid biopsy for cancer diagnosis, surveillance and treatment.
When cfDNA is released by cancer cells, it is specifically called ctDNA (circulating tumor DNA). Normally, these fragments are cleaned up by macrophages but in cases of cancer it is believed that the overproduction of cells leaves more cfDNA behind. Previous studies have suggested that ctDNA can reflect tumor burden and guide potential therapeutic targets.
Status of cfDNA and ctDNA research
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.
cfDNA extraction workflow
cfDNA is an extremely difficult sample type to work with because cfDNA is often limited in yield and highly fragmented. This is where MagVigen (Cat #K61003) comes into play. It can produce higher yield and higher quality NGS library (vs. Qiagen Kit).
Figure 1. cfDNA extraction workflow.
How can we help?
The quality of cfDNA sample will strongly influence the downstream applications, which makes it a critical step in library preparation.
MagVigen does high molecular weight cfDNA extraction and DNA sizing and cleanup
The studies discussed above and many other studies strongly support the necessity of continuous improvement and refinement of cfDNA extraction and DNA fragment size selection to enhance the 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 Kit and DNA sizing and cleanup nanobeads are popular choices for high molecular weight molecules 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 firstname.lastname@example.org to increase the potential applications of cfDNA and ctDNA for discovery research of tumor biology, clinical diagnostics, earlier cancer detection and targeted cancer therapy.