Pre-analytical Requirements for Analyzing Nucleic Acids from Blood

Messaoudi, Safia El; Thierry, Alain R.

doi:10.1007/978-94-017-9168-7_3

Cited by 3 publications

(1 citation statement)

References 55 publications

(57 reference statements)

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“…Knowing cirDNA size is of great interest for a better understanding of their structure(s) and origin(s) that can be related to a particular tumor physiological/biological state, leading to a higher diagnostic value. Unfortunately, the lack of harmonization of the methods used for pre-analytical procedures has led to many controversies in the literature and has not permitted the drawing of clear conclusions in this area [ 1 , 160 – 163 ]. As has already been discussed, the most reported size corresponding to mononucleosomes and oligonucleosomes [ 1 , 108 , 112 ] in the literature, has become the basic premise concerning the structure of cirDNA for many years.…”

Section: Biological Aspects Of Cirdnamentioning

confidence: 99%

Origins, structures, and functions of circulating DNA in oncology

Thierry¹,

Messaoudi²,

Gahan³

et al. 2016

Cancer Metastasis Rev

639

604

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While various clinical applications especially in oncology are now in progress such as diagnosis, prognosis, therapy monitoring, or patient follow-up, the determination of structural characteristics of cell-free circulating DNA (cirDNA) are still being researched. Nevertheless, some specific structures have been identified and cirDNA has been shown to be composed of many “kinds.” This structural description goes hand-in-hand with the mechanisms of its origins such as apoptosis, necrosis, active release, phagocytosis, and exocytose. There are multiple structural forms of cirDNA depending upon the mechanism of release: particulate structures (exosomes, microparticles, apoptotic bodies) or macromolecular structures (nucleosomes, virtosomes/proteolipidonucleic acid complexes, DNA traps, links with serum proteins or to the cell-free membrane parts). In addition, cirDNA concerns both nuclear and/or mitochondrial DNA with both species exhibiting different structural characteristics that potentially reveal different forms of biological stability or diagnostic significance. This review focuses on the origins, structures and functional aspects that are paradoxically less well described in the literature while numerous reviews are directed to the clinical application of cirDNA. Differentiation of the various structures and better knowledge of the fate of cirDNA would considerably expand the diagnostic power of cirDNA analysis especially with regard to the patient follow-up enlarging the scope of personalized medicine. A better understanding of the subsequent fate of cirDNA would also help in deciphering its functional aspects such as their capacity for either genometastasis or their pro-inflammatory and immunological effects.

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Section: Biological Aspects Of Cirdnamentioning

confidence: 99%

Origins, structures, and functions of circulating DNA in oncology

Thierry¹,

Messaoudi²,

Gahan³

et al. 2016

Cancer Metastasis Rev

639

604

View full text Add to dashboard Cite

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Methodological Variables in the Analysis of Cell-Free DNA

Bronkhorst

Aucamp

Pretorius

2016

Advances in Experimental Medicine and Biology

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In recent years, cell-free DNA (cfDNA) analysis has received increasing amounts of attention as a potential non-invasive screening tool for the early detection of genetic aberrations and a wide variety of diseases, especially cancer. However, except for some prenatal tests and BEAMing, a technique used to detect mutations in various genes of cancer patients, cfDNA analysis is not yet routinely applied in clinical practice. Although some confusing biological factors inherent to the in vivo setting play a key part, it is becoming increasingly clear that this struggle is mainly due to the lack of an analytical consensus, especially as regards quantitative analyses of cfDNA. In order to use quantitative analysis of cfDNA with confidence, process optimization and standardization are crucial. In this work we aim to elucidate the most confounding variables of each preanalytical step that must be considered for process optimization and equivalence of procedures.

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Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA

et al. 2021

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Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.

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Pre-analytical Requirements for Analyzing Nucleic Acids from Blood

Cited by 3 publications

References 55 publications

Origins, structures, and functions of circulating DNA in oncology

Origins, structures, and functions of circulating DNA in oncology

Methodological Variables in the Analysis of Cell-Free DNA

Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA

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