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Rajar P, Åsegg-Atneosen M, Saugstad OD, Solberg R, Baumbusch LO. Quantification of circulating cell-free DNA (cfDNA) in urine using a newborn piglet model of asphyxia. PLoS One 2020; 14:e0227066. [PMID: 31891615 PMCID: PMC6938324 DOI: 10.1371/journal.pone.0227066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/10/2019] [Indexed: 12/03/2022] Open
Abstract
Cell free DNA (cfDNA) in plasma has been described as a potential diagnostic indicator for a variety of clinical conditions, including neonatal hypoxia. Neonatal hypoxia or perinatal asphyxia is a severe medical condition caused by a temporary interruption in oxygen availability during birth. Previously, we have reported temporal changes of cfDNA detected in blood in a newborn piglet model of perinatal asphyxia. However, cfDNA can also be found in other body liquids, opening for a less invasive diagnostic prospective. The objective of this study was to test and establish a reliable method for the isolation and quantification of cfDNA from urine and to explore changes in the quantities of cfDNA using a newborn piglet model of asphyxia. Animals were exposed to hypoxia-reoxygenation (n = 6), hypoxia-reoxygenation + hypothermia (n = 6) or were part of the sham-operated control group (n = 6) and urine samples (n = 18) were collected at 570 minutes post-intervention. Two alternative applications of cfDNA measurement were tested, an indirect method comprising a centrifugation step together with DNA extraction with magnetic beads versus a direct assessment based on two centrifugation steps. CfDNA concentrations were determined by a fluorescent assay using PicoGreen and by qRT-PCR. Genomic (gDNA) and mitochondrial DNA (mtDNA) cfDNA were determined in parallel, taking into account potential differences in the rates of damages caused by oxidative stress. In contrast to previous publications, our results indicate that the direct method is insufficient. Application of the indirect method obtained with the fluorescence assay revealed mean cfDNA levels (SD) of 1.23 (1.76) ng/ml for the hypoxia samples, 4.47 (6.15) ng/ml for the samples exposed to hypoxia + hypothermia and 2.75 (3.62) ng/ml for the control animals. The mean cfDNA levels in piglets exposed to hypoxia + hypothermia revealed significantly higher cfDNA amounts compared to mean cfDNA levels in the samples purely exposed to hypoxia (p < 0.05); however, no significant difference could be determined when compared to the control group (p = 0.09). Application of the indirect method by qRT-PCR revealed mean cfDNA levels of mtDNA and gDNA at the detection limit of the technique and thus no reliable statistics could be performed between the observed cfDNA levels in the investigated groups. The methodology for detection and monitoring of cfDNA in urine has to be further optimized before it can be applied in a clinical setting in the future.
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Affiliation(s)
- Polona Rajar
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Monica Åsegg-Atneosen
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Ola Didrik Saugstad
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Rønnaug Solberg
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Pediatrics, Vestfold Hospital Trust, Tønsberg, Norway
| | - Lars Oliver Baumbusch
- Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
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Molnár B, Galamb O, Kalmár A, Barták BK, Nagy ZB, Tóth K, Tulassay Z, Igaz P, Dank M. Circulating cell-free nucleic acids as biomarkers in colorectal cancer screening and diagnosis - an update. Expert Rev Mol Diagn 2019; 19:477-498. [PMID: 31046485 DOI: 10.1080/14737159.2019.1613891] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Screening methods for one of the most frequently diagnosed malignancy, colorectal cancer (CRC), have limitations. Circulating cell-free nucleic acids (cfNA) hold clinical relevance as screening, prognostic and therapy monitoring markers. Area covered: In this review, we summarize potential CRC-specific cfNA biomarkers, the recently developed sample preparation techniques, their applications, and pitfalls. Expert opinion: Automated extraction of cfDNA is highly reproducible, however, cfDNA yield is less compared to manual isolation. Quantitative and highly sensitive detection techniques (e.g. digital PCR, NGS) can be applied to analyze genetic and epigenetic changes. Detection of DNA mutations or methylation in cfDNA and related altered levels of mRNA, miRNA, and lncRNA may improve early cancer recognition, based on specific, CRC-related patterns. Detection of cfDNA mutations (e.g. TP53, KRAS, APC) has limited diagnostic sensitivity (40-60%), however, methylated DNA including SEPT9, SFRP1, SDC2 can be applied with higher sensitivity (up to 90%) for CRC. Circulating miRNAs (e.g. miR-21, miR-92, miR-141) provide comparably high sensitivity for CRC as the circulating tumor cell mRNA markers (e.g. EGFR, CK19, CK20, CEA). Automation of cfNA isolation coupled with quantitative analysis of CRC-related, highly sensitive biomarkers may enhance CRC screening and early detection in the future.
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Affiliation(s)
- Béla Molnár
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.,b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Orsolya Galamb
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.,b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Alexandra Kalmár
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.,b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Barbara Kinga Barták
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Zsófia Brigitta Nagy
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Kinga Tóth
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Zsolt Tulassay
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.,b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Péter Igaz
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.,b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Magdolna Dank
- c Department of Oncology , Semmelweis University , Budapest , Hungary
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Barták BK, Kalmár A, Galamb O, Wichmann B, Nagy ZB, Tulassay Z, Dank M, Igaz P, Molnár B. Blood Collection and Cell-Free DNA Isolation Methods Influence the Sensitivity of Liquid Biopsy Analysis for Colorectal Cancer Detection. Pathol Oncol Res 2018; 25:915-923. [PMID: 29374860 DOI: 10.1007/s12253-018-0382-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/05/2018] [Indexed: 02/08/2023]
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Ziza KC, Liao AW, Dezan M, Dinardo CL, Jens E, Francisco RPV, Junior AM, Zugaib M, Levi JE. Determination of Fetal RHD Genotype Including the RHD Pseudogene in Maternal Plasma. J Clin Lab Anal 2016; 31. [PMID: 27595845 DOI: 10.1002/jcla.22052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/09/2016] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE To examine the accuracy of fetal RHD genotype and RHD pseudogene determination in a multiethnical population. METHODS Prospective study involving D-negative pregnant women. Cell-free DNA was extracted from 1 ml of maternal plasma by an automated system (MagNA Pure Compact, Roche) and real-time PCR was performed in triplicate targeting the RHD gene exons 5 and 7. Inconclusive samples underwent RHD pseudogene testing by real-time PCR analysis employing novel primers and probe. RESULTS A positive result was observed in 128/185 (69.2%) samples and negative in 50 (27.0%). Umbilical cord blood phenotype confirmed all cases with a positive or negative PCR result. Seven (3.8%) cases were found inconclusive (exon 7 amplification only) and RHD pseudogene testing with both conventional and real-time PCR demonstrated a positive result in five of them, while two samples were also RHD pseudogene negative. CONCLUSION Real-time PCR targeting RHD exons 5 and 7 simultaneously in maternal plasma is an accurate method for the diagnosis of fetal D genotype in our population. The RHD pseudogene real-time PCR assay is feasible and is particularly useful in populations with a high prevalence of this allele.
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Affiliation(s)
| | - Adolfo Wenjaw Liao
- Department of Obstetrics and Gynecology, Hospital das Clínicas, São Paulo University Medical School, São Paulo, Brazil
| | - Marcia Dezan
- Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, Brazil
| | | | - Eduardo Jens
- Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, Brazil
| | | | | | - Marcelo Zugaib
- Department of Obstetrics and Gynecology, Hospital das Clínicas, São Paulo University Medical School, São Paulo, Brazil
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Rather RA, Saha SC, Dhawan V. The Most Favourable Procedure for the Isolation of Cell-Free DNA from the Plasma of Iso-Immunized RHD-Negative Pregnant Women. J Circ Biomark 2015; 4:12. [PMID: 28936248 PMCID: PMC5548194 DOI: 10.5772/62113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/26/2015] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The ability to achieve quality recovery of cell-free foetal DNA is important for making non-invasive prenatal diagnoses. In this study, we performed quantitative and qualitative analyses of isolated DNA from maternal plasma, using different DNA-isolation methods. METHOD DNA was isolated from 30 iso-immunized women via the QIAamp column-based method, using four different elution volumes and two conventionally based methods. Real-time polymerase chain-reaction quantification of RHD and β-globin genes was performed in order to determine foetal-specific sequences and total genome equivalents, respectively. RESULTS The column-based method at a 3 μl elution volume yielded the highest quality and quantity of total DNA (67.0±0.6 ng/μL). At a 3 μl elution volume, the β-globin and RHD-gene sequences were estimated to be the highest among all isolation procedures, with 2778.13±1.5 and 66.9±0.6 GEq/mL, respectively, and a 100% sensitivity for RHD-gene sequence detection. Among the two conventional manual methods, the boiling lysis method yielded a higher DNA concentration (53.8±0.8 ng/μL) and purity (1.73±0.05). In addition, the method's sensitivity for foetal-detection sequences was only 80%, whereas the salting-out method's sensitivity was just 70%. CONCLUSIONS This study confirms the theory that the QIAamp method is a specific and sensitive approach for purifying and quantifying plasma DNA, when used in the minimum elution volume.
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Affiliation(s)
- Riyaz Ahmad Rather
- Department of Obstetrics and Gynaecology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Subhas Chandra Saha
- Department of Obstetrics and Gynaecology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Veena Dhawan
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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Breitbach S, Sterzing B, Magallanes C, Tug S, Simon P. Direct measurement of cell-free DNA from serially collected capillary plasma during incremental exercise. J Appl Physiol (1985) 2014; 117:119-30. [DOI: 10.1152/japplphysiol.00002.2014] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To investigate the kinetics of cell-free DNA (cfDNA) due to exercise, we established a direct real-time PCR for the quantification of cfDNA from unpurified capillary plasma by amplification of a 90- and a 222-bp multilocus L1PA2 sequence. Twenty-six male athletes performed an incremental treadmill test. For cfDNA measurement, capillary samples were collected serially from the fingertip preexercise, during, and several times postexercise. Venous blood was drawn before and immediately after exercise to compare capillary and venous cfDNA values. To elucidate the strongest association of cfDNA accumulations with either cardiorespiratory or metabolic function during exercise, capillary cfDNA values were correlated with standard measures like heart rate, oxygen consumption, or lactate concentrations. The venous cfDNA concentrations were significantly higher compared with the capillary plasma, but in both fractions cfDNA increased 9.8-fold and the values correlated significantly ( r = 0.796). During incremental treadmill running, the capillary cfDNA concentrations increased nearly parallel to the lactate values. The values correlated best with heart rate and energy expenditure, followed by oxygen consumption, Borg values, and lactate levels (0.710 ≤ r ≥ 0.808). With this article, we present a sensitive procedure for the direct quantification of cfDNA in unpurified capillary plasma instead of purified venous plasma. Further studies should investigate the differences between capillary and venous cfDNA that might mirror different physiological mechanisms. Enhanced cardiorespiratory function during exercise might lead to the accumulation of cfDNA via the release of stress hormones that already increase at intensities below the anaerobic threshold. Furthermore, cfDNA might be released by neutrophil extracellular traps.
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Affiliation(s)
- Sarah Breitbach
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Björn Sterzing
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Carlos Magallanes
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Suzan Tug
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University Mainz, Mainz, Germany
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Breitbach S, Tug S, Helmig S, Zahn D, Kubiak T, Michal M, Gori T, Ehlert T, Beiter T, Simon P. Direct quantification of cell-free, circulating DNA from unpurified plasma. PLoS One 2014; 9:e87838. [PMID: 24595313 PMCID: PMC3940427 DOI: 10.1371/journal.pone.0087838] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/30/2013] [Indexed: 02/06/2023] Open
Abstract
Cell-free DNA (cfDNA) in body tissues or fluids is extensively investigated in clinical medicine and other research fields. In this article we provide a direct quantitative real-time PCR (qPCR) as a sensitive tool for the measurement of cfDNA from plasma without previous DNA extraction, which is known to be accompanied by a reduction of DNA yield. The primer sets were designed to amplify a 90 and 222 bp multi-locus L1PA2 sequence. In the first module, cfDNA concentrations in unpurified plasma were compared to cfDNA concentrations in the eluate and the flow-through of the QIAamp DNA Blood Mini Kit and in the eluate of a phenol-chloroform isoamyl (PCI) based DNA extraction, to elucidate the DNA losses during extraction. The analyses revealed 2.79-fold higher cfDNA concentrations in unpurified plasma compared to the eluate of the QIAamp DNA Blood Mini Kit, while 36.7% of the total cfDNA were found in the flow-through. The PCI procedure only performed well on samples with high cfDNA concentrations, showing 87.4% of the concentrations measured in plasma. The DNA integrity strongly depended on the sample treatment. Further qualitative analyses indicated differing fractions of cfDNA fragment lengths in the eluate of both extraction methods. In the second module, cfDNA concentrations in the plasma of 74 coronary heart disease patients were compared to cfDNA concentrations of 74 healthy controls, using the direct L1PA2 qPCR for cfDNA quantification. The patient collective showed significantly higher cfDNA levels (mean (SD) 20.1 (23.8) ng/ml; range 5.1–183.0 ng/ml) compared to the healthy controls (9.7 (4.2) ng/ml; range 1.6–23.7 ng/ml). With our direct qPCR, we recommend a simple, economic and sensitive procedure for the quantification of cfDNA concentrations from plasma that might find broad applicability, if cfDNA became an established marker in the assessment of pathophysiological conditions.
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Affiliation(s)
- Sarah Breitbach
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Suzan Tug
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Susanne Helmig
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Daniela Zahn
- Department of Health Psychology, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Thomas Kubiak
- Department of Health Psychology, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Matthias Michal
- Department of Psychosomatic Medicine and Psychotherapy, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Tommaso Gori
- Department of Cardiology, Angiology and Internal Medicine, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Tobias Ehlert
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Thomas Beiter
- Department of Sports Medicine, Medical Clinic, Eberhard-Karls-University of Tuebingen, Tuebingen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
- * E-mail:
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Holmberg RC, Gindlesperger A, Stokes T, Lopez D, Hyman L, Freed M, Belgrader P, Harvey J, Li Z. Akonni TruTip(®) and Qiagen(®) methods for extraction of fetal circulating DNA--evaluation by real-time and digital PCR. PLoS One 2013; 8:e73068. [PMID: 23936545 PMCID: PMC3735556 DOI: 10.1371/journal.pone.0073068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/30/2013] [Indexed: 12/18/2022] Open
Abstract
Due to the low percentage of fetal DNA present in maternal plasma (< 10%) during early gestation, efficient extraction processes are required for successful downstream detection applications in non-invasive prenatal diagnostic testing. In this study, two extraction methods using similar chemistries but different workflows were compared for isolation efficiency and percent fetal DNA recovery. The Akonni Biosystems TruTip technology uses a binding matrix embedded in a pipette tip; the Circulating Nucleic Acids Kit from Qiagen employs a spin column approach. The TruTip method adds an extra step to decrease the recovery of DNA fragments larger than 600 bp from the sample to yield an overall higher percentage of smaller molecular weight DNA, effectively enriching for fetal DNA. In this evaluation, three separate extraction comparison studies were performed - a dilution series of fragmented DNA in plasma, a set of clinical maternal samples, and a blood collection tube time point study of maternal samples. Both extraction methods were found to efficiently extract small fragment DNA from large volumes of plasma. In the amended samples, the TruTip extraction method was ~15% less efficient with overall DNA recovery, but yielded an 87% increase in % fetal DNA relative to the Qiagen method. The average percent increase of fetal DNA of TruTip extracted samples compared to the Qiagen method was 55% for all sets of blinded clinical samples. A study comparing extraction efficiencies from whole blood samples incubated up to 48 hours prior to processing into plasma resulted in more consistent % fetal DNA recoveries using TruTip. The extracted products were tested on two detection platforms, quantitative real-time PCR and droplet digital PCR, and yielded similar results for both extraction methods.
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Banzola I, Kaufmann I, Lapaire O, Hahn S, Holzgreve W, Rusterholz C. Isolation of serum nucleic acids for fetal DNA analysis: comparison of manual and automated extraction methods. Prenat Diagn 2009; 28:1227-31. [PMID: 19039825 DOI: 10.1002/pd.2154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
OBJECTIVES To investigate the performance of an automated system for the extraction of cell-free DNA of maternal and fetal origin from stored serum samples for subsequent quantitative real-time polymerase chain reaction (PCR) analysis. METHODS Thirty-two maternal blood samples between the early second trimester and term were obtained. Cell-free DNA was extracted from replicate stored sera using a column-based manual isolation procedure and with an automated system, the MagNA Pure LC Instrument. Real-time quantitative PCR for the ubiquitous glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and male-specific DYS14 loci was performed. RESULTS The extraction yields for both total and fetal DNA and the quality of the purified nucleic acids were similar for the automated system or the manual procedure. However, the number of false-negative results in samples collected early in pregnancy was reduced with the automated extraction. Furthermore, the extraction rate by the automated system was highly reproducible over time. CONCLUSIONS We validated the use of an automated extraction system for the isolation of fetal DNA from stored serum. This procedure might be exploited in the future for high-throughput non-invasive fetal gene analysis of archived serum samples.
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Affiliation(s)
- Irina Banzola
- Laboratory for Prenatal Medicine and Gynecologic Oncology, Department of Biomedicine, University Hospital, Basel, Switzerland
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Huang DJ, Mergenthaler-Gatfield S, Hahn S, Holzgreve W, Zhong XY. Isolation of cell-free DNA from maternal plasma using manual and automated systems. Methods Mol Biol 2008; 444:203-208. [PMID: 18425482 DOI: 10.1007/978-1-59745-066-9_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cell-free fetal DNA present in the maternal circulation holds great potential for noninvasive prenatal diagnosis and analysis of fetal genetic traits. However, only approximately 3-6% of total DNA in the maternal plasma is of fetal origin. Because of its scarcity in the maternal circulation, various methods have been developed and tested to optimize the extraction of this rare material from plasma. Here, we first describe the commonly used protocol for separating plasma from whole blood samples. We also describe two commercially available methods for the extraction of cell-free DNA from maternal plasma, which we have found particularly straightforward and easy to use: a manual method using the High Pure PCR Template Preparation kit (Roche Diagnostics) and an automated system using the MagNA Pure LC instrument (Roche Diagnostics). Use of the methods described here will help to ensure maximum yield and purity of cell-free fetal DNA extracted from maternal plasma samples for downstream analyses.
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Affiliation(s)
- Dorothy J Huang
- Laboratory of Prenatal Medicine, University Women's Hospital/Department of Research, Basel, Switzerland
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Horinek A, Korabecna M, Panczak A, Gallova ZU, Nouzova K, Calda P, Hancarova M. Cell-Free Fetal DNA in Maternal Plasma during Physiological Single Male Pregnancies: Methodology Issues and Kinetics. Fetal Diagn Ther 2008; 24:15-21. [DOI: 10.1159/000132400] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 02/09/2007] [Indexed: 11/19/2022]
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12
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Li Y, Finning K, Daniels G, Hahn S, Zhong X, Holzgreve W. Noninvasive genotyping fetal Kell blood group (KEL1) using cell-free fetal DNA in maternal plasma by MALDI-TOF mass spectrometry. Prenat Diagn 2008; 28:203-8. [DOI: 10.1002/pd.1936] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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13
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Clausen FB, Krog GR, Rieneck K, Dziegiel MH. Improvement in fetal DNA extraction from maternal plasma. Evaluation of the NucliSens Magnetic Extraction system and the QIAamp DSP Virus Kit in comparison with the QIAamp DNA Blood Mini Kit. Prenat Diagn 2007; 27:6-10. [PMID: 17154236 DOI: 10.1002/pd.1605] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Prenatal diagnostic assays have been developed using free fetal DNA circulating in the maternal blood of pregnant women. Efficient DNA extraction is crucial for a robust analysis. To improve fetal DNA yield, we tested two manual extraction methods--the NucliSens Magnetic Extraction (NMAG) system and the QIAamp DSP Virus Kit (QDSP)--against our current standard method, the widely used QIAamp DNA Blood Mini Kit (QDNA). METHODS The fetal DNA yield of the two extraction systems was evaluated using the RHD exon 7 as target in DNA extracts of 75 plasma samples from pregnant RhD-negative women, known to have given birth to RhD-positive infanto. The total DNA yield was evaluated in 23 samples, targeting GAPDH. RESULTS The fetal DNA yield was improved by a mean factor of 1.7 using the NMAG system, and improved by a mean factor of 1.5 using the QDSP. The total DNA yield was improved by a mean factor of 2.3 using the NMAG system, and by a mean factor of 1.3 using the QDSP. CONCLUSION Both extraction systems tested were superior to our standard with regard to DNA yield. This improvement may have a great impact on the success of genotyping in early pregnancy.
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Maron JL, Bianchi DW. Prenatal diagnosis using cell-free nucleic acids in maternal body fluids: A decade of progress. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2007; 145C:5-17. [PMID: 17299735 DOI: 10.1002/ajmg.c.30115] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ability to detect cell-free fetal nucleic acids in pregnant women has greatly evolved over the past decade. Dozens of papers have explored the biology, kinetics, and clinical significance of both cell-free fetal DNA and mRNA in the maternal circulation. As a result, our overall understanding of fetal nucleic acid trafficking has expanded. To date, two applications, gender determination and fetal RhD status, have translated into clinical medicine. However, with advanced molecular techniques such as mass spectrometry, real-time quantitative polymerase chain reaction, and gene expression arrays, the ease with which fetal genes can be detected within the mother has greatly improved. Newly identified placental and fetal mRNA transcripts as well as an epigenetically modified placental DNA marker, maspin, have universal applicability. Global expression analyses of fetal mRNA in both amniotic fluid and blood provide new insights into fetal development and pathology. Prenatal diagnosis is poised to evolve from detection of aneuploidy to detection of deviation from normal development, which should provide novel opportunities for fetal treatment.
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Affiliation(s)
- Jill L Maron
- Department of Pesiatrics, Tufts-New England Center, Boston, MA 02111, USA.
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Li Y, Holzgreve W, Kiefer V, Hahn S. MALDI-TOF Mass Spectrometry Compared With Real-Time PCR for Detection of Fetal Cell-Free DNA in Maternal Plasma. Clin Chem 2006; 52:2311-2. [PMID: 17138855 DOI: 10.1373/clinchem.2006.076257] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Jorgez CJ, Dang DD, Simpson JL, Lewis DE, Bischoff FZ. Quantity versus quality: Optimal methods for cell-free DNA isolation from plasma of pregnant women. Genet Med 2006; 8:615-9. [PMID: 17079877 DOI: 10.1097/01.gim.0000241904.32039.6f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
PURPOSE Methods to isolate cell-free fetal DNA from maternal plasma are critical in developing noninvasive fetal DNA testing strategies. Given that plasma consists of heterogeneous DNA-size fragments in a complex mix of proteins, recovery and analysis of this DNA are understandably inefficient. To facilitate recovery, we performed qualitative and quantitative analysis of DNA isolated from maternal plasma. METHODS DNA isolated from maternal blood (n = 15) was compared using five different DNA isolation protocols: two conventional, two column-based, and one magnetic-bead based. Purity and concentration of DNA recovered were determined with a NanoDrop spectrophotometer. Real-time polymerase chain reaction quantification of the beta-globin and DYS1 loci was performed to determine total and fetal-specific genome equivalents, respectively. RESULTS DNA quality and quantity were different among the five methods tested. Although purity and concentration of total DNA were greatest with the conventional boiling-lysis approach, correct detection of a male fetus was achieved in only 62.5% of cases. DNA isolation using the magnetic beads yielded the highest quantity of total DNA (2018.83 +/- 4.09 GEq/mL), with 100% fetal DNA detection. CONCLUSIONS Optimal plasma DNA recovery protocols must take into account DNA purity and concentration. We confirm that the magnetic-beads method provides a fast, simple, sensitive, and specific approach to purify plasma DNA. The resulting high-quality DNA facilitates efficient examination of fetal DNA sequences.
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Affiliation(s)
- Carolina J Jorgez
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas 77054, USA
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