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, 4 (7), e00699
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Factors That Influence Quality and Yield of Circulating-Free DNA: A Systematic Review of the Methodology Literature

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Factors That Influence Quality and Yield of Circulating-Free DNA: A Systematic Review of the Methodology Literature

R M Trigg et al. Heliyon.

Abstract

Background: Circulating-free DNA (cfDNA) is under investigation as a liquid biopsy of cancer for early detection, monitoring disease progression and therapeutic response. This systematic review of the primary cfDNA literature aims to identify and evaluate factors that influence recovery of cfDNA, and to outline evidence-based recommendations for standardization of methods.

Methods: A search of the Ovid and Cochrane databases was undertaken in May 2018 to obtain relevant literature on cfDNA isolation and quantification. Retrieved titles and abstracts were reviewed by two authors. The factors evaluated include choice of specimen type (plasma or serum); time-to-processing of whole blood; blood specimen tube; centrifugation protocol (speed, time, temperature and number of spins); and methods of cfDNA isolation and quantification.

Findings: Of 4,172 articles identified through the database search, 52 proceeded to full-text review and 37 met the criteria for inclusion. A quantitative analysis was not possible, due to significant heterogeneity in methodological approaches between studies. Therefore, included data was tabulated and a textual qualitative synthesis approach was taken.

Interpretation: This is the first systematic review of methodological factors that influence recovery and quantification of cfDNA, enabling recommendations to be made that will support standardization of methodological approaches towards development of blood-based cancer tests.

Keywords: Oncology.

Figures

Fig. 1
Fig. 1
Number of publications by year relating to cfDNA in cancer between 1995 and 2017. The search was conducted in PubMed using search terms combined with Boolean operators, as follows: (ccfDNA OR cfDNA OR cfNA OR ctDNA OR cell-free DNA OR cell free DNA OR cell-free serum DNA OR circulating DNA OR circulating free DNA OR circulating-free DNA OR circulating nucleic acids OR circulating tumor DNA OR free DNA OR free tumor DNA OR plasma DNA OR plasma tumor DNA OR ptDNA OR serum DNA OR serum cell-free) AND (cancer OR neoplas* OR tumor). Publications relating to cell-free DNA in non-blood analytes (e.g. urine and ascites) and cell culture media were not included. A yearly breakdown of publication types is presented in Supplemental Table S1.
Fig. 2
Fig. 2
Methodological variables in processing and analysis of cfDNA.
Fig. 3
Fig. 3
PRISMA flow diagram of literature search and inclusion/exclusion process.

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