Cell-free DNA (cfDNA) is now widely studied as a marker of disease prognosis or to facilitate the detection of therapeutic targets in various diseases, particularly cancer. Most dermatological studies focus on melanoma, followed by other skin diseases such as vascular malformations and psoriasis. 

Genetic alterations unique to the tissue of origins, such as sequence variations, copy number alterations, chromosomal rearrangements, differential DNA methylation patterns and fragmentation patterns, can be detected in circulation, furnishing information on patient disease status. Polymerase chain reaction (PCR)-based methods and next-generation sequencing (NGS) detect these alterations depending on the target of interest. 

A recent study describes the origins of cfDNA, the common methods of detection, the role of cfDNA as a biomarker, and its potential clinical applications in melanoma and other skin diseases. 

cfDNA can be collected in samples with any bodily fluid, with plasma as the commonest source. However, rare targets of interest may require higher fluid volume and DNA input. In cases of unsuccessful plasma separation from whole blood within a few hours, using specialized collection tubes with stabilizing reagents is adviced.

Droplet digital PCR(ddPCR) is frequently used in melanoma studies to detectmutated BRAF and/or NRAS alleles as potential biomarkers of disease burden and/or response to treatment. It provides absolute quantification of rare alleles; and has the highest sensitivity and specificity of available PCR-based methods. Yet the limitation of ddPCR is- they generally require previous knowledge of the target of interest and are often limited to detecting a single mutant and wild-type allele.

NGS methods can however detect numerous targets. Further, it can also identify alterations in a small panel of targets or for broad coverage such as whole-exome or whole-genome analysis. Yet its limitations are- not providing precise quantification owing to the library preparation and sequencing methodologies; having higher limits of detection than ddPCR; and mutational analysis of cfDNA may be confounded by nontumor mutations originating from aging normal lymphocytic cells (i.e., clonal hematopoiesis).

Source: Wiggins JM, Ali S, Polsky D. Cell-free DNA in dermatology research. J Invest Dermatol. 2022;142(6):P1523-8.e1.