Liquid biopsy - Performance of the PAXgene® Blood ccfDNA Tubes for the isolation and characterization of cell-free plasma DNA from tumor patients

Schmidt, Bernd; Reinicke, Dana; Reindl, I; Bork, I; Wollschläger, B; Lambrecht, Nils; Fleischhacker, Michael

doi:10.1016/j.cca.2017.03.031

Cited by 33 publications

(14 citation statements)

References 21 publications

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“…Recently, an abstract from Qiagen indicated that Streck tubes may contain formaldehyde which can induce DNA deaminations and introduce bias in cfDNA methylation analyses [40]. Furthermore, PAXgene ccfDNA tubes allow unbiased quantification of methylated sequences to be performed and are therefore fitfor-purpose for downstream cfDNA methylation analyses [41]. The concern that the Streck tube preservative might introduce DNA sequence modifications was recently dismissed by Risberg et al who showed that there is no difference in background error rate between cfDNA extracted from Streck BCT and from paired EDTA samples and analyzed by Tagged Amplicon deep sequencing (Tam-Seq) [42••].…”

Section: Critical Ex Vivo Pre-analytical Factorsmentioning

confidence: 99%

Biospecimen Science of Blood for cfDNA Genetic Analyses

Ammerlaan

Betsou

2019

Curr Pathobiol Rep

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Purpose of Review cfDNA is increasingly used for biomonitoring oncological diseases or pregnancy status by different genetic analyses. Uncontrolled pre-analytical variability impacts the quality and quantity and subsequently undermines the utility of this analyte. In this review, we summarize critical pre-analytical factors to be addressed, to avoid irreproducible results. Recent Findings cfDNA quantity and quality can be impacted by the in vivo condition of the donor and the ex vivo biospecimen handling prior to the downstream analysis. In vivo, physical and psychosocial stress, circadian rhythmicity, and age appear to be critical. Ex vivo, the blood collection tubes, pre-centrifugation storage temperature and time, and cfDNA extraction kits are important. Summary To address these critical pre-analytical viabilities, in-process quality control material should be applied. Plasma is preferred to serum, as are blood collection tubes with stabilizers. Finally, the donor status and sample processing should be standardized and documented.

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Section: Critical Ex Vivo Pre-analytical Factorsmentioning

confidence: 99%

Biospecimen Science of Blood for cfDNA Genetic Analyses

Ammerlaan

Betsou

2019

Curr Pathobiol Rep

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“…Some unclarity exists about the compatibility of the stabilization technology in Streck Tubes with epigenetic tests requiring bisulfite treatment prior to qPCR. Schmidt et al [ 77 ••] mentioned that the Streck Tube does not seem to work for this application. According to Distler et al [ 78 ], methylated SEPT9 colorectal cancer screening marker can be detected with almost 100% sensitivity in blood from EDTA tubes stored at 2–8 °C for a maximum of 24 h, as well as in blood from CPDA tubes stored at 18–25 °C for up to 48 h using the Epi proColon (Epigenomics, Berlin, Germany) colorectal cancer screening test.…”

Section: Preservation Solutions For Improving and Standardizing Pre-amentioning

confidence: 99%

“…The stabilization reagent in the tube is free of cross-linking or cross-linker-releasing substances ( www.preanalytix.com ) and hence does not chemically modify ccfDNA. Schmidt et al [ 77 ••] evaluated the PAXgene Blood ccfDNA System, including manual and automated extraction, for the quantification of methylated mSHOX2 plasma DNA in lung cancer patients. They found that total yield of ccfDNA was stabilized in PAXgene tubes when samples were stored for 7 days at room temperature and quantification of methylated mSHOX2 sequence by qPCR following bisulfite treatment was possible.…”

Section: Preservation Solutions For Improving and Standardizing Pre-amentioning

confidence: 99%

Liquid Biopsy Preservation Solutions for Standardized Pre-Analytical Workflows—Venous Whole Blood and Plasma

et al. 2018

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Purpose of ReviewLiquid biopsy analyses based on circulating cell-free nucleic acids, circulating tumor cells or other diseased cells from organs, and exosomes or other microvesicles in blood offer new means for non-invasive diagnostic applications. The main goal of this review is to explain the importance of preserving whole blood specimens after blood draw for use as liquid biopsies, and to summarize preservation solutions that are currently available.Recent FindingsDespite the great potential of liquid biopsies for diagnostics and disease management, besides non-invasive prenatal testing (NIPT), only a few liquid biopsy applications are fully implemented for routine in vitro diagnostic testing. One major barrier is the lack of standardized pre-analytical workflows, including the collection of consistent quality blood specimens and the generation of good-quality plasma samples therefrom. Broader use of liquid biopsies in clinical routine applications therefore requires improved pre-analytical procedures to enable high-quality specimens to obtain unbiased analyte profiles (DNA, RNA, proteins, etc.) as they are in the patient’s body.SummaryA growing number of stabilizing reagents and dedicated blood collection tubes are available for the post-collection preservation of circulating cell-free DNA (ccfDNA) profiles in whole blood. In contrast, solutions for the preservation of circulating tumor cells (CTC) that enable both, enumeration and molecular analyses are rare. Solutions for extracellular vesicle (EV) populations, including exosomes, do not yet exist.

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“…From a technical standpoint, blood collection is conducted in specific vessels coated with stabilizing agents that prevent contamination with genomic DNA originating from nucleated blood cell lysis [ 145 ]. The most commonly used solutions, largely implemented in clinical studies [ 146 , 147 , 148 , 149 ], are provided by Streck (Cell-free DNA BCT), Qiagen (PAXgene Blood ccfDNA Tubes) and Roche (CE-IVD Cell-free DNA Collection Tube). Ethylenediaminetetraacetic acid (EDTA) tubes, typically costing less than 1/10 of the aforementioned solutions, can be used as a valid alternative [ 150 ].…”

Section: Liquid Biopsy In Current Clinical Practicementioning

confidence: 99%

Cancer Diagnosis Using a Liquid Biopsy: Challenges and Expectations

et al. 2018

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The field of cancer diagnostics has recently been impacted by new and exciting developments in the area of liquid biopsy. A liquid biopsy is a minimally invasive alternative to surgical biopsies of solid tissues, typically achieved through the withdrawal of a blood sample or other body fluids, allowing the interrogation of tumor-derived material including circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) fragments that are present at a given time point. In this short review, we discuss a few studies that summarize the state-of-the-art in the liquid biopsy field from a diagnostic perspective, and speculate on current challenges and expectations of implementing liquid biopsy testing for cancer diagnosis and monitoring in the clinical setting.

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Liquid biopsy - Performance of the PAXgene® Blood ccfDNA Tubes for the isolation and characterization of cell-free plasma DNA from tumor patients

Cited by 33 publications

References 21 publications

Biospecimen Science of Blood for cfDNA Genetic Analyses

Biospecimen Science of Blood for cfDNA Genetic Analyses

Liquid Biopsy Preservation Solutions for Standardized Pre-Analytical Workflows—Venous Whole Blood and Plasma

Cancer Diagnosis Using a Liquid Biopsy: Challenges and Expectations

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