Circulating tumor DNA – Current state of play and future perspectives

Abstract

Cancer management paradigms are shifting towards a personalized approach thanks to the advent of the -omics technologies. Liquid biopsies, consisting in the sampling of blood and other bodily fluids, are emerging as a valid alternative to circulating tumor biomarkers and tumor tissue biopsies for cancer diagnosis, routine monitoring and prognostication. The content of a liquid biopsy is referred to as the "tumor circulome". Among its components, circulating tumor DNA (ctDNA), including both cell-free and exosome-associated DNA, is the most widely characterized element. ctDNA analysis has a tremendous capability in the diagnostic arena. Its potential has been demonstrated at each level of disease staging and management and supported by a recent FDA approval for companion diagnostic, and the investments being made by pharmaceutical companies in this sector are numerous. The approaches available for ctDNA analysis allow both quantitative and qualitative studies and range from PCR and dPCR-mediated single/multiple gene mutational assessment to whole genome next generation sequencing and methylation mapping. Although the principal object of a liquid biopsy is blood, other body fluids such as urine and saliva show potential as complementary DNA sources for tumor analysis. In this review we provide a synopsis on the state of play of current ctDNA application. We discuss the clinical significance of ctDNA analysis and review the state of the art of technologies being currently developed to this aim. We also discuss the current issues limiting ctDNA application and highlight the promising approaches being developed to overcome these.

Interest of circulating tumor DNA as a biomarker for canine cancers: illustration in histiocytic sarcoma, oral malignant melanoma and multicentric lymphoma

“…In human oncology, current studies focus on the analysis of DNA released from tumor cells in plasma (ctDNA), which is much more cancer-specific. Today one ctDNA assay for the detection of EGFR mutation in patients with non-small cell lung cancer (NSCLC ) has been approved by the Food and Drug Administration, and ctDNA assays for EGFR in NSCLC and KRAS in colorectal cancer are available for commercial use in Europe 3,4,54 . As in human, ctDNA has also been found in some canine cancers such as lymphoma 20 , mammary carcinoma 50 and more recently in pulmonary adenocarcinoma 52 .…”

“…Cell-free DNA (cfDNA) circulates in plasma and other body fluids such as urine, cerebrospinal fluid, pleural fluid and saliva as short double-stranded DNA fragments of about 160 base pairs. In healthy patients, cfDNA is released during cell deaths like apoptosis or necrosis, or by active secretion, and comes mainly from the hematopoietic lineage with minimal contributions from other tissues [1][2][3][4] . Since its first discovery in human in 1948 5 , it was shown that cfDNA in the blood reflects various pathological processes such as inflammatory disease, sepsis, trauma, stroke and cancer, and its concentration is correlated with disease severity and prognosis 2,[6][7][8] .…”

Novel molecular insights and new therapeutic strategies in osteosarcoma

“…Determining tumor proliferation and metastases in CTCs are performed using DNA methylation [ 162 ]. Furthermore, ctDNA technologies provide a series of analyses including single gene mutational evaluation, next generation deep genome sequencing, following analysis of methylation, where their application covers all stages of cancer management [ 163 ].…”

“…Its sensitivity for early detection can be limited by low amount of ctDNA because of low tumor burden, leading to 0.02% MAF sensitivity. A number of advanced technologies can facilitate methods required for enhancement of the sensitivity including unique molecular identifiers (UMIs) in the amplification step preceding sequencing and the in vitro and in silico improvement of ctDNA using virtue of shorter fragment length of them [ 163 ].…”

Analysis of the Whole-Exome Sequencing of Tumor and Circulating Tumor DNA in Metastatic Melanoma

“…Analysis of circulating tumor DNA (ctDNA) can be used to identify therapeutically actionable mutations, monitor disease progression, detect residual disease and track the genomic evolution of treatment resistance [1][2][3][4]. The genomic profiling of ctDNA using whole genome, whole exome or targeted sequencing is feasible, but technically challenging due to the low quantities and fragmented nature of ctDNA [5][6][7][8].…”