New Perspectives for Liquid Profiling of Circulating Nucleic Acids in Clinical Diagnostics

New Perspectives for Liquid Profiling of Circulating Nucleic Acids in Clinical Diagnostics

Abstract
Liquid profiling of molecular characteristics of circulating nucleic acids (CNAs) in the blood and other bodily fluids is one of the most interesting, dynamic and promising areas in laboratory diagnostics. In recent years the field has expanded rapidly in various directions and is about to reach routine clinical application in non-invasive prenatal testing, oncology and transplantation medicine. With the optimization of new technologies such as massive parallel sequencing, standardization and rigorous quality control, disease-specific enrichment of nucleic acids, combination of diverse molecular characteristics and advanced bioinformatic pipelines, the diagnostic power of liquid profiling has been considerably increased. It also has become evident that a better understanding of the biology, structure, function and metabolism of CNAs is crucial for improving the diagnostic process and for accurate interpretation of the results. Valuable diagnostic information is particularly provided by genetic and epigenetic changes of cell-free DNA, but RNA, miRNA and extravesicular (ev) CNA patterns gain increasing interest, too.
In prenatal medicine, the identification of chromosomal aberrations and some genetic diseases on fetal DNA in maternal blood plasma is widely established. In cancer disease, profiling mutations in circulating tumor (ct) DNA is meaningful for the stratification of patients to specific targeted therapies and can also be applied for monitoring therapy response, detecting minimal residual disease, characterizing the clonal evolution and thus being used as a “real” companion diagnostic for patient guidance through the disease. In transplantation medicine, donor CNA can be sensitively detected in the blood plasma of the graft recipient which is associated with the occurrence of complications, graft failure and poor prognosis. In infectious diseases, CNA diagnostics are used for the characterization of the pathogen, the antibiotic resistance as well as the host reaction and prognosis during sepsis. New approaches in the CNA field include the utilization of epigenetic patterns on CNA, fragmentomics and deconvolution for tissue-of-origin diagnostics. Moreover, the role of neutrophil extracellular traps (NETs) for inflammatory, septic and thrombotic pathologies gains momentum. It is recognized from regulatory bodies that standardization of high-throughput technologies and (pre-) analytical processes, use of appropriate quality controls and professional reporting is essential to ensure sensitive and accurate CNA diagnostics for patient care. Developments in recent years show convincingly that CNA diagnostics will be a valuable and versatile tool in the future clinical laboratory setting.