Technologies for Size-Based Analysis of Circulating Cell-Free DNA: Limitations and Clinical Implementation

Abstract

Prostate cancer is the second most common malignancy in men worldwide, and incidence is likely to rise in the next decade. The current screening options have limitations and have been shown to result in over-treatment of clinically insignificant disease. New biomarkers and technologies to detect them are therefore needed to better diagnose and stratify patients in primary care.Circulating cell-free DNA (ccfDNA) has gained interest as a potential minimally invasive biomarker, detectable in many bodily fluids (such as blood, urine, and cerebral spinal fluid) and reflecting the mutational landscape in tumours.More recently, the size distribution of ccfDNA fragments has also gained interest as a specific biomarker, where differences in size distribution have been observed between healthy volunteers and cancer patients, resulting in the new field of fragmentomics. Analysis of ccfDNA sizes provides avenues for alternative analytical technologies but commercial options are currently limited. Most focus on mutation detection and are subject to several biases that may affect size distribution.Here we discuss the available technologies and identify major issues and considerations that may affect their implementation as a clinically useful test based on ccfDNA size profiling.

Exploring the Role of Circulating Cell-Free DNA in Disease Diagnosis and Therapy

“…Typically, ccfDNA fragments are small, often ranging from 150 to 200 base pairs, corresponding to the size of DNA wrapped around a nucleosome. This size pattern suggests that ccfDNA fragmentation is a regulated process, likely associated with apoptosis, where enzymes systematically break down the DNA into these characteristic sizes [17]. However, variations in size distribution are observed in different pathological conditions, including cancer, where larger fragments might be present due to the mechanisms of cell death in tumors or the active release of DNA by cancer cells.…”