Potential of modern circulating cell-free DNA diagnostic tools for detection of specific tumour cells in clinical practice

Abstract

Personalized medicine is a developing field of medicine that has gained in importance in recent decades. New diagnostic tests based on the analysis of circulating cell-free DNA (cfDNA) were developed as a tool of diagnosing different cancer types. By detecting the subpopulation of mutated DNA from cancer cells, it is possible to detect the presence of a specific tumour in early stages of the disease. Mutation analysis is performed by quantitative polymerase chain reaction (qPCR) or the next generation sequencing (NGS), however, cfDNA protocols need to be modified carefully in preanalytical, analytical, and postanalytical stages. To further improve treatment of cancer the Food and Drug Administration approved more than 20 companion diagnostic tests that combine cancer drugs with highly efficient genetic diagnostic tools. Tools detect mutations in the DNA originating from cancer cells directly through the subpopulation of cfDNA, the circular tumour DNA (ctDNA) analysis or with visualization of cells through intracellular DNA probes. A large number of ctDNA tests in clinical studies demonstrate the importance of new findings in the field of cancer diagnosis. We describe the innovations in personalized medicine: techniques for detecting ctDNA and genomic DNA (gDNA) mutations approved Food and Drug Administration companion genetic diagnostics, candidate genes for assembling the cancer NGS panels, and a brief mention of the multitude of cfDNA currently in clinical trials. Additionally, an overview of the development steps of the diagnostic tools will refresh and expand the knowledge of clinics and geneticists for research opportunities beyond the development phases.

Klinische Anwendungsbeispiele einer Next-Generation-Sequencing-basierten Multi-Genpanel-Analyse

“…Targeted Sequencing) eignet sich besonders gut für die Diagnostik solcher hereditären Krebserkrankungen [15]. Die zirkulierende Tumor-DNA im peripheren Blut resultiert aus nekrotisierenden oder apoptotischen Tumorzellen und liefert wertvolle Informationen über somatische Mutationen und Keimzellmutationen [18]. Der Nachweis von ursächlichen Keimbahnmutationen aus peripherem Blut ermöglicht die rasche Detektion und prädiktive genetische Testung hochgradig gefährdeter Familienmitglieder [14].…”

Klinische Anwendungsbeispiele einer Next-Generation-Sequencing-basierten Multi-Genpanel-Analyse

“…Targeted Sequencing) eignet sich besonders gut für die Diagnostik solcher hereditären Krebserkrankungen [15]. Die zirkulierende Tumor-DNA im peripheren Blut resultiert aus nekrotisierenden oder apoptotischen Tumorzellen und liefert wertvolle Informationen über somatische Mutationen und Keimzellmutationen [18]. Der Nachweis von ursächlichen Keimbahnmutationen aus peripherem Blut ermöglicht die rasche Detektion und prädiktive ge-▶ Tab.…”

Harnessing Liquid Biopsies to Guide Immune Checkpoint Inhibitor Therapy

“…The total number of somatic mutations per DNA megabase (Mb), also known as tumor mutational burden (TMB), is an independent predictor of response to IO across multiple cancer types [ 75 , 76 ]. Biological processes contributing to elevated TMB can result from environmental factors such as exposure to cigarette smoke and ultraviolet radiation, or from deleterious mutations in mismatch repair leading to microsatellite instability, or in the DNA repair machinery [ 77 , 78 ]. In order to determine TMB, a large number of genes must be sequenced, typically more than 300 genes, which are then analysed to determine the number of non-synonymous mutations per mega base pair (Mbp).…”