Comparison of Roche Cell-Free DNA collection Tubes to Streck Cell-Free DNA BCT s for sample stability using healthy volunteers

Parackal, Sarah; Zou, Donghui; Day, Robert C.; Black, Michael A.; Guilford, Parry

doi:10.1016/j.plabm.2019.e00125

Cited by 22 publications

(18 citation statements)

References 20 publications

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“…9,14,15 Indeed, DNA extraction prior to plasma cfDNA measurement is commonplace in human studies, across multiple DNA quantification methods. 1,14,16,19 Therefore, we feel that our results with extracted-plasma cfDNA are a significant contribution to our understanding of this biomarker in horses. Our results show that median extracted-plasma cfDNA was significantly higher in emergency cases, and a subset of emergencies with colic, compared to healthy horses.…”

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confidence: 99%

Investigation of plasma cell-free DNA as a potential biomarker in horses

2022

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Plasma cell-free DNA (cfDNA) is a biomarker of ischemia, systemic inflammation, and mortality in humans with gastrointestinal disease. Cell-free DNA has not been investigated as a biomarker for equine colic, to our knowledge. We hypothesized that cfDNA could be measured accurately in neat equine plasma using a benchtop fluorometer and that plasma cfDNA would be elevated in emergency patients compared to healthy horses. Plasma was obtained from blood collected in Roche DNA stabilizing tubes. We used the Qubit 4 fluorometer and 1× dsDNA HS assay kit to measure cfDNA concentration in neat patient plasma and following DNA extraction of plasma with a commercial kit. Assay precision and linearity of dilution were satisfactory for neat plasma cfDNA, but DNA spike and recovery results were variable. Further, cfDNA concentrations in paired neat plasma and extracted-plasma samples ( n = 66) were not correlated. Median extracted-plasma cfDNA was higher in emergency patients ( n = 50) and a subgroup of colic patients ( n = 36), compared to healthy horses ( n = 19). Our results with extracted-plasma samples provide proof of concept for further investigation of plasma cfDNA as a biomarker in horses.

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confidence: 99%

Investigation of plasma cell-free DNA as a potential biomarker in horses

2022

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“…To monitor the size distribution of the plasma DNA and therefore define the degree of contamination with high molecular cellular DNA, we analyzed the fragment size of the extracted plasma DNA using a Bio-Analyzer 2100. Circulating tumor DNA (ctDNA) has a fragment size of 90–250bp, while high-molecular cellular DNA, probably from lysed immune cells, are high molecular fragments clustering at the length of ≥1000 bp [ 21 ]. Fragment size analysis suggested that only a minor fraction of the isolated plasma DNA was in the range expected for ctDNA ( Figure 1 B).…”

Section: Resultsmentioning

confidence: 99%

“…Other studies suggested that utilization of Cell-Free DNA BCT tubes (Streck, La Vista, Nebraska) or PaxGene tubes (Qiagen, Hilden, Germany) significantly decrease contamination of the ctDNA with cellular DNA [ 13 , 20 ] by preventing cell damage due to cell-preserving reagents. However, even with the usage of such specific sample tubes, lysis of peripheral blood lymphocytes (PBLs) is not completely abolished [ 21 ]. The data presented here clearly show that our purification procedure is capable of rescuing such contaminated plasma DNA samples.…”

Section: Discussionmentioning

confidence: 99%

Rescue of Non-Informative Circulating Tumor DNA to Monitor the Mutational Landscape in NSCLC

Mayer¹,

Schmidtke-Schrezenmeier

Buske

et al. 2020

Cancers

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In non-small cell lung cancer (NSCLC) the usage of plasma-derived circulating tumor DNA (ctDNA) have come into focus to obtain a comprehensive genetic profile of a given lung cancer. Despite the usage of specific sampling tubes, archived plasma samples as well as inappropriately treated blood samples still cause a loss of information due to cell lysis and contamination with cellular DNA. Our aim was to establish a reliable protocol to rescue ctDNA from such non-informative samples to monitor the mutational landscape in NSCLC. As a proof-of-concept study we used archived plasma samples derived from whole blood EDTA samples of 51 patients suffering from NSCLC. Analysis of the isolated plasma DNA determined only a small fraction of ctDNA in a range of 90–250 bp. By applying a specific purification procedure, we were able to increase the informative ctDNA content and improve in a cohort of 42 patients the detection of driver mutations from 32% to 79% of the mutations found in tissue biopsies. Thus, we present here an easy to perform, time and cost effective procedure to rescue non-informative ctDNA samples, which is sufficient to detect oncogenic mutations in NGS approaches and is therefore a valuable technical improvement for laboratories handling liquid biopsy samples.

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“…When compared to EDTA, and considering the effectivity of cell lysis prevention, claimed utilities of the available systems were proved in several studies, including the Streck Cell-Free DNA BCT tubes [ 13 , 26 , 91 , 92 , 93 , 95 , 103 , 104 ], the CellSave Preservative tubes (CellSearch, Huntington Valley, PA, USA) [ 97 , 105 ], the Qiagen PAXgene Blood ccfDNA Tube [ 92 , 106 ], the Roche Cell-Free DNA Collection Tubes [ 12 , 98 , 107 ], the Norgen cf-DNA/cf-RNA Preservative Tubes [ 96 ] and Biomatrica LBgard Blood Tube [ 108 , 109 , 110 ]. Studies listing limitations are, however, also available.…”

Section: Sample Collectionmentioning

confidence: 99%

Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

Pös

Styk

et al. 2020

IJMS

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Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.

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Comparison of Roche Cell-Free DNA collection Tubes to Streck Cell-Free DNA BCT s for sample stability using healthy volunteers

Cited by 22 publications

References 20 publications

Investigation of plasma cell-free DNA as a potential biomarker in horses

Investigation of plasma cell-free DNA as a potential biomarker in horses

Rescue of Non-Informative Circulating Tumor DNA to Monitor the Mutational Landscape in NSCLC

Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes

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