Comparison of 4 commercial kits for the extraction of circulating DNA from plasma

Warton, Kristina; Graham, Lisa-Jane K.; Yuwono, Nicole Laurencia; Samimi, Goli

doi:10.1016/j.cancergen.2018.02.004

Cited by 56 publications

(34 citation statements)

References 30 publications

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“…We summarize the characteristics of each kit in Table 1. QC specializes in cfDNA extraction, and many researchers have reported its efficient purification performance [17][18][19]. The QC has also been widely used for liquid biopsy using urinary cfDNA in various urologic and non-urologic malignancies [5,[28][29][30].…”

Section: Discussionmentioning

confidence: 99%

“…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%

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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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Section: Discussionmentioning

confidence: 99%

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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“…Fresh plasma should be stored at −20 or −80 ℃ (on dry ice for shipping), with long-term stability of DNA in plasma best demonstrated at −80 ℃ (86,88). Specifically designed methods for DNA extraction are essential, and several kits are now commercially available (55,86,90).…”

Section: Sample Collection and Stewardshipmentioning

confidence: 99%

Molecular testing strategies in non-small cell lung cancer: optimizing the diagnostic journey

Gregg

Yoneda

2019

Transl. Lung Cancer Res

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Molecular testing identifies patients with advanced non-small cell lung cancer (NSCLC) who may benefit from targeted therapy or immunotherapy (i.e., immune checkpoint inhibitor treatment for patients with high tumor mutational burden (TMB), microsatellite instability-high or mismatch repairdeficient tumors). Current guidelines state that molecular testing should be conducted at the time of initial diagnosis and tumor progression on targeted therapy. In real-world clinical practice in the United States (US), molecular testing is often not conducted or happens late in the diagnostic journey, resulting in delayed or inappropriate treatment. Herein, we review the rationale for molecular testing in advanced NSCLC, along with best-practice guidelines based on published recommendations and our own clinical experience, including a case study. We propose three strategies to optimize molecular testing in newly diagnosed patients with advanced NSCLC: (I) pulmonologists, interventional radiologists, or thoracic surgeons order molecular tests as soon as advanced NSCLC with an adenocarcinoma component is suspected; (II) liquid biopsies conducted early in the diagnostic pathway; and (III) pathologist-directed reflex testing, as conducted in other areas of oncology. To help facilitate these strategies, we outline our recommendations for optimal sample collection techniques and stewardship. In summary, we believe that implementation of these individual strategies will allow clinicians to effectively leverage available treatment options for advanced NSCLC, reducing the time to optimal treatment and improving patient outcomes.

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“…However, the feasibility of applying these methods has in the past been affected by the potential for direct exposure of hazardous chemicals to operators and the significant time involved. However, the availability of commercial DNA extraction kits has markedly reduced these limitations and improved the quality and yield of isolated DNA [ 59 , 60 ]. The protocols involve techniques such as spin column-based purification and magnetic bead DNA separation.…”

Section: Dna-based Diagnostics For Schistosomiasismentioning

confidence: 99%

DNA Diagnostics for Schistosomiasis Control

2018

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Despite extensive efforts over the last few decades, the global disease burden of schistosomiasis still remains unacceptably high. This could partly be attributed to the lack of accurate diagnostic tools for detecting human and animal schistosome infections in endemic areas. In low transmission and low prevalence areas where schistosomiasis elimination is targeted, case detection requires a test that is highly sensitive. Diagnostic tests with low sensitivity will miss individuals with low infection intensity and these will continue to contribute to transmission, thereby interfering with the efficacy of the control measures operating. Of the many diagnostic approaches undertaken to date, the detection of schistosome DNA using DNA amplification techniques including polymerase chain reaction (PCR) provide valuable adjuncts to more conventional microscopic and serological methods, due their accuracy, high sensitivity, and the capacity to detect early pre-patent infections. Furthermore, DNA-based methods represent important screening tools, particularly in those endemic areas with ongoing control where infection prevalence and intensity have been reduced to very low levels. Here we review the role of DNA diagnostics in the path towards the control and elimination of schistosomiasis.

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Comparison of 4 commercial kits for the extraction of circulating DNA from plasma

Cited by 56 publications

References 30 publications

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

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

Molecular testing strategies in non-small cell lung cancer: optimizing the diagnostic journey

DNA Diagnostics for Schistosomiasis Control

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