Quantifying Cell Free DNA in Urine: Comparison Between Commercial kits, Impact of Gender and Inter-Individual Variation

Streleckiene, Greta; Reid, Hayley M; Arnold, Norbert; Bauerschlag, Dirk; Förster, Michael

doi:10.2144/btn-2018-0003

Cited by 36 publications

(33 citation statements)

References 13 publications

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“…From these results, one can conclude that bead-based isolation methods worked somewhat better than membrane-based kits and that the former ones are especially useful for the isolation of low-molecularweight DNA. A similar conclusion was recently reported for the isolation of cfDNA from urine [45]. It is important to keep in mind that the DNA yield and purity of these "dedicated" kits show a high variability depending on the method of the isolation procedure.…”

Section: Dna Isolationsupporting

confidence: 83%

“…When they looked for differences in these markers in serum samples obtained on different days (day 1, 8, 15, 22 and 29), the intra-individual variation was 12.7% and 11.5% for 5mC and H3K9Me3, respectively. A similar observation was reported for the amount of cfDNA in urine [45]. The quantity of cfDNA from male and female healthy subjects, which was isolated over several days, demonstrated a large day-to-day variation in both sexes (the urine was collected always at the same time of the day, i.e.…”

Section: Basic Principles Of Cell-free Nucleic Acids: Release Half-lsupporting

confidence: 81%

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Pre-analytical issues in liquid biopsy – where do we stand?

Fleischhacker

Schmidt

2020

Journal of Laboratory Medicine

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It is well documented that in the chain from sample to the result in a clinical laboratory, the pre-analytical phase is the weakest and most vulnerable link. This also holds for the use and analysis of extracellular nucleic acids. In this short review, we will summarize and critically evaluate the most important steps of the pre-analytical phase, i.e. the choice of the best control population for the patients to be analyzed, the actual blood draw, the choice of tubes for blood drawing, the impact of delayed processing of blood samples, the best method for getting rid of cells and debris, the choice of matrix, i.e. plasma vs. serum vs. other body fluids, and the impact of long-term storage of cell-free liquids on the outcome. Even if the analysis of cell-free nucleic acids has already become a routine application in the area of non-invasive prenatal screening (NIPS) and in the care of cancer patients (search for resistance mutations in the EGFR gene), there are still many unresolved issues of the pre-analytical phase which need to be urgently tackled.

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Section: Dna Isolationsupporting

confidence: 83%

Section: Basic Principles Of Cell-free Nucleic Acids: Release Half-lsupporting

confidence: 81%

Pre-analytical issues in liquid biopsy – where do we stand?

Fleischhacker

Schmidt

2020

Journal of Laboratory Medicine

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“…In addition, urinary cfDNA also reflects the systemic status of patients, as it is derived from both the urinary tract and the circulatory system [16]. However, although many studies have compared the various extraction methods of circulating cfDNA in blood [17][18][19], limited data are available on methods for urinary cfDNA extraction [20,21]. Most studies have been conducted on urinary DNA, regardless of being genomic DNA or cfDNA [22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions

Lee

Yoon

et al. 2020

Diagnostics

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Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection.

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“…Thus, the longer DNA fragments were considered as genomic DNA (gDNA) mostly likely originated from lysed hematopoietic cells [13,14]. DNA fragments [16][17][18].…”

Section: Discussionmentioning

confidence: 99%

Quantification of Cell-Free DNA: A Comparative Study of Three Different Methods

Jeon

Lee

et al. 2019

J Lab Med Qual Assur

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Cell-free DNA (cfDNA) is a subset of circulating extracellular DNA in plasma, which is released from cells mostly through apoptosis, necrosis, and active secretion [1]. The cfDNA is easily obtained by using minimally invasive procedures and has unique potential biomarkers for non-invasive prenatal testing and cancer management [2,3]. The recent advances in molecular technologies such as next-generation sequencing (NGS) and digital polymerase chain reaction (dPCR) have enabled routine analysis in clinical laboratories [4]. The standardization of the analytical conditions to detect the genetic alterations in cfDNA still remains a major challenge [5]. After isolation from plasma, cfDNA is quantified before downstream analysis (e.g., NGS and dPCR). An accurate measurement of cfDNA, as a stringent quality control of cfDNA isolation, is a critical preliminary step for these downstream analyses [6]. Several methods have been described to quantify cfDNA. Quantitative PCR (qPCR) has been used to measure DNA concentration by targeting various pre-selected DNA sequences, and recently more rapid and costeffective methods such as spectrophotometry, fluorometry, and electrophoresis-based methods are being used [5].

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Quantifying Cell Free DNA in Urine: Comparison Between Commercial kits, Impact of Gender and Inter-Individual Variation

Cited by 36 publications

References 13 publications

Pre-analytical issues in liquid biopsy – where do we stand?

Pre-analytical issues in liquid biopsy – where do we stand?

Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions

Quantification of Cell-Free DNA: A Comparative Study of Three Different Methods

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