Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations

Bronkhorst, Abel J.; Ungerer, Vida; Holdenrieder, Stefan

doi:10.1080/10408363.2019.1700902

Cited by 36 publications

(28 citation statements)

References 157 publications

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“…11 However, barring these exciting developments, thousands of studies attest that the development of clinically meaningful cfDNA-based tests is complicated significantly by a lack of knowledge concerning the molecular origin and physical features of cfDNA. 3,12 This poor understanding is mainly a result of the difficulty to study the biological properties of specific cfDNA molecules within a highly complex and nucleic acidheterogeneous biospecimen such as blood-a direct consequence of the inherent complexity of an in vivo system. Therefore, owing to the relative simplicity of two-dimensional (2D) cell culture models and the high level of variable control that such in vitro experiments offer, some researchers are exploring this approach as an alternative or auxiliary avenue for elucidating the biological properties of cfDNA.…”

Section: Introductionmentioning

confidence: 99%

Comparison of methods for the isolation of cell-free DNA from cell culture supernatant

2020

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In vitro characterization of cell-free DNA using two-dimensional cell culture models is emerging as an important step toward an improved understanding of the physical and biological characteristics of cell-free DNA in human biology. However, precise measurement of the cell-free DNA in cell culture medium is highly dependent on the efficacy of the method used for DNA purification, and is often a juncture of experimental confusion. Therefore, in this study, we compared six commercially available cell-free DNA isolation kits for the recovery of cell-free DNA from the cell culture supernatant of a human bone cancer cell line (143B), including two magnetic bead-based manual kits, one automated magnetic bead-based extraction method, and three manual spin-column kits. Based on cell-free DNA quantitation and sizing, using the Qubit dsDNA HS assay and Bioanalyzer HS DNA assay, respectively, the different methods showed significant variability concerning recovery, reproducibility, and size discrimination. These findings highlight the importance of selecting a cell-free DNA extraction method that is appropriate for the aims of a study. For example, mutational analysis of cell-free DNA may be enhanced by a method that favors a high yield or is biased toward the isolation of short cell-free DNA fragments. In contrast, quantitative analysis of cell-free DNA in a comparative setting (e.g. measuring the fluctuation of cell-free DNA levels over time) may require the selection of a cell-free DNA isolation method that forgoes a high recovery for high reproducibility and minimal size bias.

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Section: Introductionmentioning

confidence: 99%

Comparison of methods for the isolation of cell-free DNA from cell culture supernatant

2020

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“…single-molecule resolutions. However, based on theoretical calculations assuming that ctDNA release is proportional to tumor mass, 4 ml of blood plasma is likely to contain less than one cancer genomes if the tumor is smaller than approximately 1 cm 3 , which corresponds to an early-stage tumor detectable by imaging in a symptomatic patient [143,144]. With few ctDNA molecules expected per ml plasma, there are two options to increase the likelihood of detecting cancer: (i) increase liquid biopsy volume or (ii) increase number of potential mutations that can be detected [58,145], where the last alternative is the most feasible.…”

Section: Screeningmentioning

confidence: 99%

Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations

Andersson

Kristiansson

Kubista

et al. 2021

Expert Review of Molecular Diagnostics

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Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation. Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications. Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.

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“…An increasing number of studies have demonstrated the potential use of cell-free DNA (cfDNA) as a potential biomarker in cancer for diagnosis, prognosis, and follow-up (Bronkhorst, Ungerer, & Holdenrieder, 2019). Up to date, 3 studies investigated cfDNA in MTC and are reported in Table 9.…”

Section: Cell-free Dna (Cfdna) As Biomarker In Mtcmentioning

confidence: 99%

Role of tissue and circulating microRNAs and DNA as biomarkers in medullary thyroid cancer

Chiacchiarini

Trocchianesi

Besharat

et al. 2021

Pharmacology & Therapeutics

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations

Cited by 36 publications

References 157 publications

Comparison of methods for the isolation of cell-free DNA from cell culture supernatant

Comparison of methods for the isolation of cell-free DNA from cell culture supernatant

Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations

Role of tissue and circulating microRNAs and DNA as biomarkers in medullary thyroid cancer

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