Circulating free DNA

Circulating free DNA (cfDNA) (also known as cell-free DNA) are degraded DNA fragments released to body fluids such as blood plasma, urine, cerebrospinal fluid, etc. Typical sizes of cfDNA fragments reflect chromatosome particles (~165bp), as well as multiples of nucleosomes, which protect DNA from digestion by apoptotic nucleases.^[1] The term cfDNA can be used to describe various forms of DNA freely circulating in body fluids, including circulating tumor DNA (ctDNA), cell-free mitochondrial DNA (ccf mtDNA), cell-free fetal DNA (cffDNA) and donor-derived cell-free DNA (dd-cfDNA).^[2] Elevated levels of cfDNA are observed in cancer, especially in advanced disease.^[3] There is evidence that cfDNA becomes increasingly frequent in circulation with the onset of age.^[4] cfDNA has been shown to be a useful biomarker for a multitude of ailments other than cancer and fetal medicine. This includes but is not limited to trauma, sepsis, aseptic inflammation, myocardial infarction, stroke, transplantation, diabetes, and sickle cell disease.^[5] cfDNA is mostly a double-stranded extracellular molecule of DNA, consisting of small fragments (50 to 200 bp) ^[6][7] and larger fragments (21 kb) ^[8] and has been recognized as an accurate marker for the diagnosis of prostate cancer and breast cancer.^[9]

Recent studies have laid the foundation for inferring gene expression from cell-free DNA, with EPIC-seq emerging as a notable advancement.^[10] This method has substantially raised the bar for the noninvasive inference of expression levels of individual genes, thereby augmenting the assay's applicability in disease characterization, histological classification, and monitoring treatment efficacy.^[10][11][12]

Other publications confirm the origin of cfDNA from carcinomas and cfDNA occurs in patients with advanced cancer. Cell‐free DNA (cfDNA) is present in the circulating plasma and in other body fluids.^[13]

The release of cfDNA into the

cfDNA purification is prone to contamination through genomic DNA due to ruptured blood cells during the purification process.[34] Because of this, different purification methods can lead to significantly different cfDNA extraction yields.^[35][36] At the moment, typical purification methods involve collection of blood via venipuncture, centrifugation to pellet the cells, and extraction of cfDNA from the plasma. The specific method for extraction of cfDNA from the plasma depends on the protocol desired.^[37]

Analysis of cfDNA

PCR

In general, the detection of specific DNA sequences in cfDNA can be done by two means; sequence specific detection (PCR based) and general genomic analysis of all cfDNA present in the blood (DNA sequencing).^[38] The presence of cfDNA containing DNA from tumor cells was originally characterized using PCR amplification of mutated genes from extracted cfDNA.^[21] PCR based analysis of cfDNA typically rely on the analytical nature of qPCR and digital PCR. Both of these techniques can be sensitive and cost-effective for detecting limited number of hotspots mutations. For this reason the PCR based method of detection is still very prominent tool in cfDNA detection. This method has the limitation of not being able to detect larger structural variant present in ctDNA and for this reason massively parallel next generation sequencing is also used to determine ctDNA content in cfDNA

Massively Parallel Sequencing

Massively parallel sequencing (MPS) has allowed the deep sequencing of cfDNA. This deep sequencing is required to detect mutant ctDNA present in low concentrations in the plasma. Two main sequencing techniques are typically used for targeted analysis of mutant cfDNA; PCR amplicon sequencing^[39] and hybrid capture sequencing.^[40] Other forms of genetic alterations can be analysed using ctDNA (e.g. somatic copy number alterations or genetic rearrangements). Here, methods based on untargeted sequencing, like WGS or low coverage WGS, are mainly used.

cfDNA and Illness

Cancer

The majority of cfDNA research is focused on DNA originating from cancer (ctDNA). In short, the DNA from cancer cells gets released by cell-death, secretion or other mechanisms still not known.^[41] The fraction of cfDNA released by tumor cells in circulation is influenced by the size of the tumor as well as the tumor stage and type. Early stage cancers and brain tumor are among the most difficult to detect with liquid biopsy.^[42][43][44]

Trauma

Elevated cfDNA has been detected with acute blunt trauma^[45] and burn victims.^[46] In both of these cases cfDNA concentration in the plasma were correlated to the severity of the injury, as well as outcome of the patient.

Sepsis

It has been shown that an increase cfDNA in the plasma of ICU patients is an indicator of the onset of sepsis.^[47][48] Due to the severity of sepsis in ICU patients, further testing in order to determine the scope of cfDNA efficacy as a biomarker for septic risk is likely.^[5]

Myocardial Infarction

Patients showing signs of myocardial infarction have been shown to have elevated cfDNA levels.^[49] This elevation correlates to patient outcome in terms of additional cardiac issues and even mortality within two years.^[50]

Transplant Graft Rejection

Foreign cfDNA has been shown to be present in the plasma of solid organ transplant patients. This cfDNA is derived from the grafted organ and is termed dd-cfDNA (donor-derived cell-free DNA). Dd-cfDNA values spike initially after a transplant procedure (>5%) with values heavily depending on the transplanted organ and typically drop (<0.5%) within one week for most organs.^[51] If the host body rejects the grafted organ the ddcfDNA concentration in the blood (plasma) will rise to a level greater than 5-fold higher than those without complications. This increase in ddcfDNA can be detected prior to any other clinical or biochemical signs of complication.^[51] Besides dd-cfDNA in plasma, some research also focused on the excretion of ddcfDNA through urine. This is of special interest in kidney allografts transplantation. When dd-cfDNA is measured using targeted

NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA

References