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Elgun T, Musteri Oltulu Y, Yurttas Gok A, Agyuz U, Kilic U. DETERMINATION OF RH TYPE AND GENDER USING CIRCULATING CELL-FREE FETAL DNA IN EARLY PREGNANCY OF RH NEGATIVE WOMEN IN TURKEY. Transfus Clin Biol 2023:S1246-7820(23)00063-0. [PMID: 37116742 DOI: 10.1016/j.tracli.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023]
Abstract
INTRODUCTION Choosing the right clinical approach for early and reliable diagnosis/screening is becoming more important day by day. The aim of the study was to determine the early RhD type with cff-DNA obtained from maternal plasma, especially in the light of recent developments. In this way, it is aimed to apply Rh Ig only to mothers who are determined to have RhD (+) fetuses and to prevent unnecessary further tests that may possess a risk for RhD (-) fetuses. METHODS Prediction of fetal gender and RH genotype was performed by using RT-qPCR method. With simultaneous amplification of sequences of SRY, DYS14 and RH genes (exon 7 and exon 10). Fetal gender and RhD were determined in 30 RHD (-) pregnant women with cfDNA. RESULTS As a result of genotyping, the gender of 67% (20/30) fetuses was determined as male; the gender of 33% (10/30) fetuses was determined as female in a sample group of 30 pregnancies. It was determined that the DYS14 100% (20/20) gene was more sensitive than the SRY 97% (18/20) gene in gender determination after examining prenatal and postnatal results. As a result of the analysis, the presence of 17% (5/30) RhD (-) fetuses and 83% (25/30) RhD (+) fetuses were determined which is 100% compatible with postnatal results. DISCUSSION Detecting fetal RhD gene in maternal plasma made an important contribution to its use in non-invasive prenatal screening. This study shows that unnecessary intervention and cost can be avoided with successful genotyping analysis performed with RT-qPCR.
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Affiliation(s)
- Tugba Elgun
- Department of Medical Biology/Biruni University/Faculty of Medicine/ Istanbul, Turkey.
| | | | - Asiye Yurttas Gok
- Department of Biochemistry/ Istanbul Health and Technology University/Faculty of Pharmacy/Istanbul, Turkey.
| | | | - Ulkan Kilic
- Department of Medical Biology/University of Health Science/Hamidiye School of Medicine/Istanbul, Turkey.
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Clausen FB, Hellberg Å, Bein G, Bugert P, Schwartz D, Drnovsek TD, Finning K, Guz K, Haimila K, Henny C, O’Brien H, Orzinska A, Sørensen K, Thorlacius S, Wikman A, Denomme GA, Flegel WA, Gassner C, de Haas M, Hyland C, Ji Y, Lane WJ, Nogués N, Olsson ML, Peyrard T, van der Schoot CE, Weinstock C, Legler T. Recommendation for validation and quality assurance of non-invasive prenatal testing for foetal blood groups and implications for IVD risk classification according to EU regulations. Vox Sang 2022; 117:157-165. [PMID: 34155647 PMCID: PMC10686716 DOI: 10.1111/vox.13172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/20/2021] [Accepted: 06/04/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVES Non-invasive assays for predicting foetal blood group status in pregnancy serve as valuable clinical tools in the management of pregnancies at risk of detrimental consequences due to blood group antigen incompatibility. To secure clinical applicability, assays for non-invasive prenatal testing of foetal blood groups need to follow strict rules for validation and quality assurance. Here, we present a multi-national position paper with specific recommendations for validation and quality assurance for such assays and discuss their risk classification according to EU regulations. MATERIALS AND METHODS We reviewed the literature covering validation for in-vitro diagnostic (IVD) assays in general and for non-invasive foetal RHD genotyping in particular. Recommendations were based on the result of discussions between co-authors. RESULTS In relation to Annex VIII of the In-Vitro-Diagnostic Medical Device Regulation 2017/746 of the European Parliament and the Council, assays for non-invasive prenatal testing of foetal blood groups are risk class D devices. In our opinion, screening for targeted anti-D prophylaxis for non-immunized RhD negative women should be placed under risk class C. To ensure high quality of non-invasive foetal blood group assays within and beyond the European Union, we present specific recommendations for validation and quality assurance in terms of analytical detection limit, range and linearity, precision, robustness, pre-analytics and use of controls in routine testing. With respect to immunized women, different requirements for validation and IVD risk classification are discussed. CONCLUSION These recommendations should be followed to ensure appropriate assay performance and applicability for clinical use of both commercial and in-house assays.
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Affiliation(s)
- Frederik Banch Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
| | - Åsa Hellberg
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Sweden
| | - Gregor Bein
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig-University, Giessen, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden Württemberg – Hessen, Mannheim, Germany
| | - Dieter Schwartz
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Kirstin Finning
- National Health Service Blood and Transplant, International Blood Group Reference Laboratory, UK
| | - Katarzyna Guz
- Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | | | | | - Helen O’Brien
- Clinical Services and Research, Australian Red Cross Lifeblood, Brisbane, Australia
| | | | - Kirsten Sørensen
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Agneta Wikman
- Clinical Immunology and Transfusion Medicine Karolinska University Hospital and CLINTEC Karolinska Institutet, Stockholm, Sweden
| | - Gregory Andrew Denomme
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Versiti Blood Research Institute and Diagnostic Laboratories, Milwaukee, Wisconsin, USA
| | - Willy Albert Flegel
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Christoph Gassner
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Institute for Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Masja de Haas
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Department of Immunohaematology Diagnostic Services, Sanquin Diagnostic Services and Sanquin Research, Amsterdam, The Netherlands
- Department of Haematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Catherine Hyland
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Clinical Services and Research, Australian Red Cross Lifeblood, Brisbane, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Yanli Ji
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Guangzhou Blood Center, Institute of Clinical Blood Transfusion, Guangzhou, China
| | - William J. Lane
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Núria Nogués
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Immunohematology Laboratory, Blood and Tissue Bank, Barcelona, Spain
| | - Martin L. Olsson
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Sweden
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Thierry Peyrard
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Institut National de la Transfusion Sanguine, Centre National de Référence pour les Groupes Sanguins, Paris, France
| | - C. Ellen van der Schoot
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, The Netherlands
| | - Christof Weinstock
- cfDNA subgroup from the International Society of Blood Transfusion (ISBT) Working Party on Red Cell Immunogenetics and Blood Group Terminology (RCIBGT), Amsterdam, The Netherlands
- Institute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg-Hessen, and Institute of Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Tobias Legler
- Department of Transfusion Medicine, University Medical Center Göttingen, Göttingen, Germany
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Campos CDM, Childers K, Gamage SST, Wijerathne H, Zhao Z, Soper SA. Analytical Technologies for Liquid Biopsy of Subcellular Materials. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:207-229. [PMID: 33974805 PMCID: PMC8601690 DOI: 10.1146/annurev-anchem-091520-093931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Liquid biopsy markers, which can be secured from a simple blood draw or other biological samples, are used to manage a variety of diseases and even monitor for bacterial or viral infections. Although there are several different types of liquid biopsy markers, the subcellular ones, including cell-free DNA, microRNA, extracellular vesicles, and viral particles, are evolving in terms of their utility. A challenge with liquid biopsy markers is that they must be enriched from the biological sample prior to analysis because they are a vast minority in a mixed population, and potential interferences may be present in the sample matrix that can inhibit profiling the molecular cargo from the subcellular marker. In this article, we discuss existing and developing analytical enrichment platforms used to isolate subcellular liquid biopsy markers, and discuss their figures of merit such as recovery, throughput, and purity.
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Affiliation(s)
- Camila D M Campos
- Life Science Department, Imec, 3001 Leuven, Belgium
- Department of Electrical Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Katie Childers
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
| | - Sachindra S T Gamage
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Harshani Wijerathne
- Department of Mechanical Engineering, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Zheng Zhao
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
| | - Steven A Soper
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, USA;
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, Kansas 66045, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, Kansas 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
- Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
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How to Obtain a High Quality ctDNA in Lymphoma Patients: Preanalytical Tips and Tricks. Pharmaceuticals (Basel) 2021; 14:ph14070617. [PMID: 34206947 PMCID: PMC8308879 DOI: 10.3390/ph14070617] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/20/2023] Open
Abstract
The analysis of circulating tumor DNA (ctDNA) released by tumor cells holds great promise for patients with lymphoma, to refine the diagnostic procedure, clarify the prognosis, monitor the response to treatment, and detect relapses earlier. One of the main challenges of the coming years is to adapt techniques from highly specialized translational teams to routine laboratories as this requires a careful technical and clinical validation, and we have to achieve this as fast as possible to transform a promising biomarker into a routine analysis to have a direct consequence on patient care. Whatever the analytical technology used, the prerequisite is to obtain high yields of ctDNA of optimal quality. In this review, we propose a step-by-step description of the preanalytical process to obtain high-quality ctDNA, emphasizing the technical choices that need to be made and the experimental data that can support these choices.
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Diagnostic performance of the noninvasive prenatal FetoGnost RhD assay for the prediction of the fetal RhD blood group status. Arch Gynecol Obstet 2021; 304:1191-1196. [PMID: 33835210 PMCID: PMC8490250 DOI: 10.1007/s00404-021-06055-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/27/2021] [Indexed: 11/29/2022]
Abstract
Purpose To evaluate the diagnostic accuracy of a commercially available test kit for noninvasive prenatal determination of the fetal RhD status (NIPT-RhD) with a focus on early gestation and multiple pregnancies. Methods The FetoGnost RhD assay (Ingenetix, Vienna, Austria) is routinely applied for clinical decision making either in woman with anti-D alloimmunization or to target the application of routine antenatal anti-D prophylaxis (RAADP) to women with a RhD positive fetus. Based on existing data in the laboratory information system the newborn’s serological RhD status was compared with NIPT RhD results. Results Since 2009 NIPT RhD was performed in 2968 pregnant women between weeks 5 + 6 and 40 + 0 of gestation (median 12 + 6) and conclusive results were obtained in 2888 (97.30%) cases. Diagnostic accuracy was calculated from those 2244 (77.70%) cases with the newborn’s serological RhD status reported. The sensitivity of the FetoGnost RhD assay was 99.93% (95% CI 99.61–99.99%) and the specificity was 99.61% (95% CI 98.86–99.87%). No false-positive or false-negative NIPT RhD result was observed in 203 multiple pregnancies. Conclusion NIPT RhD results are reliable when obtained with FetoGnost RhD assay. Targeted routine anti-D-prophylaxis can start as early as 11 + 0 weeks of gestation in singleton and multiple pregnancies.
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Shafei N, Hakhamaneshi MS, Houshmand M, Gerayeshnejad S, Fathi F, Sharifzadeh S. Diagnostic Value of Non-Invasive Prenatal Screening of β-thalassemia by Cell Free Fetal DNA and Fetal NRBC. Curr Mol Med 2020; 19:105-111. [PMID: 30813874 DOI: 10.2174/1566524019666190226124135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 01/08/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Beta thalassemia is a common disorder with autosomal recessive inheritance. The most prenatal diagnostic methods are the invasive techniques that have the risk of miscarriage. Now the non-invasive methods will be gradually alternative for these invasive techniques. OBJECTIVE The aim of this study is to evaluate and compare the diagnostic value of two non-invasive diagnostic methods for fetal thalassemia using cell free fetal DNA (cff-DNA) and nucleated RBC (NRBC) in one sampling community. METHODS 10 ml of blood was taken in two k3EDTA tube from 32 pregnant women (mean of gestational age = 11 weeks), who themselves and their husbands had minor thalassemia. One tube was used to enrich NRBC and other was used for cff-DNA extraction. NRBCs were isolated by MACS method and immunohistochemistry; the genome of stained cells was amplified by multiple displacement amplification (MDA) procedure. These products were used as template in b-globin segments PCR. cff-DNA was extracted by THP method and 300 bp areas were recovered from the agarose gel as fetus DNA. These DNA were used as template in touch down PCR to amplify b-globin gen. The amplified b-globin segments were sequenced and the results compared with CVS resul. RESULTS The data showed that sensitivity and specificity of thalassemia diagnosis by NRBC were 100% and 92% respectively and sensitivity and specificity of thalassemia diagnosis by cff-DNA were 100% and 84% respectively. CONCLUSION These methods with high sensitivity can be used as screening test but due to their lower specificity than CVS, they cannot be used as diagnostic test.
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Affiliation(s)
- Nadia Shafei
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | | | - Massoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Siavash Gerayeshnejad
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fardin Fathi
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Sardar Sharifzadeh
- PhD student, Department of Clinical Biochemistry, School of Medicine, Tarbiat Modares University, Tehran, Iran
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Clausen FB, Barrett AN, Advani HV, Choolani M, Dziegiel MH. Impact of long-term storage of plasma and cell-free DNA on measured DNA quantity and fetal fraction. Vox Sang 2020; 115:586-594. [PMID: 32342989 DOI: 10.1111/vox.12923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Optimal sample storage conditions are essential for non-invasive prenatal testing of cell-free fetal and total DNA. We investigated the effect of long-term storage of plasma samples and extracted cfDNA using qPCR. MATERIALS AND METHODS Fetal and total cfDNA yield and fetal fraction were calculated before and after storage of plasma for 0-6 years at -25°C. Dilution experiments were performed to investigate PCR inhibition. Extraction with or without proteinase K was used to examine protein dissociation. Storage of extracted cfDNA was investigated by testing aliquots immediately, and after 18 months and 3 years of storage at -25°C. RESULTS We observed a marked increase in the levels of amplifiable fetal and total DNA in plasma stored for 2-3 years, and fetal fraction was slightly decreased after 3 years of storage. cfDNA detection was independent of proteinase K during DNA extraction in plasma samples stored >2 years, indicating a loss of proteins from DNA over time, which was likely to account for the observed increase in DNA yields. Measured fetal and total DNA quantities, as well as fetal fraction, increased in stored, extracted cfDNA. CONCLUSION Fetal and total cell-free DNA is readily detectable in plasma after long-term storage at -25°C. However, substantial variation in measured DNA quantities and fetal fraction means caution may be required when using stored plasma and extracted cfDNA for test development or validation purposes.
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Affiliation(s)
- Frederik Banch Clausen
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Henna V Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Morten Hanefeld Dziegiel
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Dauber EM, Kollmann D, Kozakowski N, Rasoul-Rockenschaub S, Soliman T, Berlakovich GA, Mayr WR. Quantitative PCR of INDELs to measure donor-derived cell-free DNA-a potential method to detect acute rejection in kidney transplantation: a pilot study. Transpl Int 2019; 33:298-309. [PMID: 31710731 PMCID: PMC7065216 DOI: 10.1111/tri.13554] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/24/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
The quantification of donor‐derived cell‐free DNA (ddcfDNA) in recipient's plasma is a novel, but technically challenging noninvasive method to assist the diagnosis of acute rejection (AR). A quantitative real‐time PCR (qPCR) approach targeting insertion/deletion polymorphisms (INDEL) was adapted to measure ddcfNA in plasma samples from 29 kidney transplant recipients obtained at time of clinically indicated biopsies (eight patients with a histologically verified AR, nine with borderline rejection and 12 without evidence of rejection). Measured ddcfDNA levels of smaller INDEL amplicon targets differed significantly (P = 0.016, Kruskal–Wallis H test) between recipients with biopsy‐proven AR (median 5.24%; range 1.00–9.03), patients without (1.50%; 0.41–6.50) and patients with borderline AR (1.91%; 0.58–5.38). Similarly, pairwise testing by Mann–Whitney U‐tests revealed significant differences between recipients with AR and without AR (P = 0.012) as well as patients with AR and borderline histology (P = 0.015). Receiver operating characteristic (ROC) analysis revealed an area under the ROC curve for discriminating AR and non‐AR biopsies of 0.84 (95% CI: 0.66–1.00). The determined cutoff value of 2.7% ddcfDNA showed a sensitivity of 0.88 (95% CI: 0.63–1.00) and specificity of 0.81 (95% CI: 0.64–0.98). INDEL qPCR represents a novel method to quantify ddcfDNA on standard qPCR instruments within 6–8 h with high sensitivity and specificity to detect AR.
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Affiliation(s)
- Eva-Maria Dauber
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Wien, Austria
| | - Dagmar Kollmann
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | | | | | - Thomas Soliman
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | - Gabriela A Berlakovich
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | - Wolfgang R Mayr
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Wien, Austria
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Akbariqomi M, Heidari R, Gargari SS, Omrani MD, Rigi G, Sanikhani NS, Kooshki H, Mahmoudian F, Mazlomi MA, Tavoosidana G. Evaluation and statistical optimization of a method for methylated cell-free fetal DNA extraction from maternal plasma. J Assist Reprod Genet 2019; 36:1029-1038. [PMID: 30820784 DOI: 10.1007/s10815-019-01425-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/18/2019] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Methylated cell-free fetal DNA (cffDNA) in maternal plasma can potentially be used as a biomarker for accurate noninvasive prenatal testing (NIPT) of fetal disorders. Recovery and purification of cffDNA are key steps for downstream applications. In this study, we aimed to developed and evaluated different aspects of an optimized method and compared its efficiency with common methods used for extraction of methylated cffDNA. METHODS Single factor experiments, Plackett-Burman (PB) design, and response surface methodology (RSM) were conducted for conventional Triton/Heat/Phenol (cTHP) method optimization. The total cell-free DNA (cfDNA) was extracted from pooled maternal plasma using the optimized method called the Triton/Heat/Phenol/Glycogen (THPG), cTHP method, a column-based kit, and a magnetic bead-based kit. In the next step, methylated cfDNA from the extracted total cfDNA was enriched using a methylated DNA immunoprecipitation (MeDIP) kit. Real-time quantitative polymerase chain reaction was performed on the RASSF1 gene and hyper region to determine the genomic equivalents per milliliter (GEq/ml) values of the methylated cfDNA and cffDNA, respectively. RESULTS The optimum values of the significant factors affecting cfDNA extraction from 200 μl of plasma were 3% SDS, 1% Triton X-100, 0.9 μg/μl glycogen, and 0.3 M sodium acetate. The GEq/ml values of methylated cffDNA extracted using the THPG method were significantly higher than for the tested extraction methods (p < 0.001). CONCLUSIONS Our results indicate that the THPG method is more efficient than the other tested methods for extraction of low copy number methylated cffDNA from a small volume of maternal plasma.
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Affiliation(s)
- Mostafa Akbariqomi
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Heidari
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soraya Saleh Gargari
- Department of Gynecology & Obstetric, Shohada Tajrish Educational Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Garshasb Rigi
- Department of Genetics, Faculty of Basic Science, Shahrekord University, Shahrekord, Iran.,Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Nafiseh Sadat Sanikhani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Kooshki
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Fatemeh Mahmoudian
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Mazlomi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Tavoosidana
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Jain M, Balatsky AV, Revina DB, Samokhodskaya LM. Direct comparison of QIAamp DSP Virus Kit and QIAamp Circulating Nucleic Acid Kit regarding cell-free fetal DNA isolation from maternal peripheral blood. Mol Cell Probes 2018; 43:13-19. [PMID: 30584912 DOI: 10.1016/j.mcp.2018.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/26/2018] [Accepted: 12/21/2018] [Indexed: 01/31/2023]
Abstract
BACKGROUND Blood of pregnant women contains cell-free fetal DNA (cffDNA), which is widely used in non-invasive prenatal diagnosis. The modern laboratory equipment market provides huge variety of commercial kits for isolation of circulating nucleic acids, but unfortunately none of them are standardized for isolation of cffDNA, which is a crucial step for success of subsequent analysis. AIM To compare DSPVK and CNAK in terms of cffDNA, cell-free total DNA (cftDNA) yield and resulting cffDNA fraction, as well as to try to explain the possible difference between the efficacy of these kits. METHODS Peripheral blood samples were collected from 18 healthy pregnant women (6th-14th week of pregnancy) and from 12 healthy unpregnant subjects. cftDNA was isolated using QIAamp Circulating Nucleic Acid Kit (CNAK) (Qiagen, Germany) and QIAamp DSP Virus Kit (DSPVK) (Qiagen, Germany) from 1 ml of plasma of each sample. Methylation-sensitive restriction was carried out to isolate cffDNA. Yield of cffDNA and cftDNA was quantified using digital PCR. To explain the difference in resulting efficacy of these two kits PCR inhibitors analysis was performed, as well as the optimal plasma input for DSPVK was investigated. RESULTS Yield of cffDNA using CNAK was statistically significantly higher than using DSPVK (167.62 (125.34-192.47) vs 52.88 (35.48-125.42) GEq/mL, p < 0.001). The same applies to cftDNA yield, CNAK appears to be statistically significantly superior to DSPVK (743.42 (455.02-898.33) vs 371.07 (294.37-509.89) GEq/mL, p < 0.001). cffDNA fraction using CNAK was also higher than using DSVPK (24.75 (14.5-31.53) vs 14.20 (6.88-25.83) %, p = 0.586), although the difference was not statistically significant due to inconsistency of DSPVK results from sample to sample. PCR inhibitors analysis uncovered increased amount of PCR inhibitors in CNAK cftDNA solution, compared to DSPVK (p = 0.002). Usage of 0.5 mL of plasma for cftDNA extraction with DSPVK over 1 mL demonstrates almost 1.8 times higher cftDNA output (p = 0.028), which suggests that this kit is not so viable for volumes of plasma larger than 0.5 mL. CONCLUSIONS We recommend CNAK over DSPVK for quantitative analysis of cffDNA. Nevertheless, DSPVK is definitely suitable for qualitative analysis as well as for research with limited budget, since it is almost 3 times cheaper than CNAK.
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Affiliation(s)
- Mark Jain
- Medical Research and Education Center, Lomonosov Moscow State University, Lomonosovsky Prospect, 27/10, 119192, Moscow, Russia.
| | | | - Daria Borisovna Revina
- Medical Research and Education Center, Lomonosov Moscow State University, Lomonosovsky Prospect, 27/10, 119192, Moscow, Russia.
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11
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Clausen FB. Lessons learned from the implementation of non-invasive fetalRHDscreening. Expert Rev Mol Diagn 2018; 18:423-431. [DOI: 10.1080/14737159.2018.1461562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Frederik Banch Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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Prenatal non-invasive foetal RHD genotyping: diagnostic accuracy of a test as a guide for appropriate administration of antenatal anti-D immunoprophylaxis. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2018; 16:514-524. [PMID: 29757138 DOI: 10.2450/2018.0270-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/13/2018] [Indexed: 11/21/2022]
Abstract
BACKGROUND Foetal RHD genotyping can be predicted by real-time polymerase chain reaction (qPCR) using cell-free foetal DNA extracted from maternal plasma. The object of this study was to determine the diagnostic accuracy and feasibility of non-invasive RHD foetal genotyping, using a commercial multiple-exon assay, as a guide to appropriate administration of targeted antenatal immunoprophylaxis. MATERIAL AND METHODS Cell-free foetal DNA was extracted from plasma of RhD-negative women between 11-30 weeks of pregnancy. The foetal RHD genotype was determined non-invasively by qPCR amplification of exons 5, 7 and 10 of the RHD gene using the Free DNA Fetal Kit® RhD. Results were compared with serological RhD cord blood typing at birth. The analysis of diagnostic accuracy was restricted to the period (24-28+6 weeks) during which foetal genotyping is usually performed for targeted antenatal immunoprophylaxis. RESULTS RHD foetal genotyping was performed on 367 plasma samples (24-28+6 weeks). Neonatal RhD phenotype results were available for 284 pregnancies. Foetal RHD status was inconclusive in 9/284 (3.2%) samples, including four cases with RhD maternal variants. Two false-positive results were registered. The sensitivity was 100% and the specificity was 97.5% (95% CI: 94.0-100). The diagnostic accuracy was 99.3% (95% CI: 98.3-100), decreasing to 96.1% (95% CI: 93.9-98.4) when the inconclusive results were included. The negative and positive predictive values were 100% (95% CI: 100-100) and 99.0% (95% CI: 97.6-100), respectively. There was one false-negative result in a sample collected at 18 weeks. After inclusion of samples at early gestational age (<23+6 week), sensitivity and accuracy were 99.6% (95% CI: 98.7-100) and 95.5% (95% CI: 93.3-97.8), respectively. DISCUSSION This study demonstrates that foetal RHD detection on maternal plasma using a commercial multiple-exon assay is a reliable and accurate tool to predict foetal RhD phenotype. It can be a safe guide for the appropriate administration of targeted prenatal immunoprophylaxis.
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Zhang S, Han S, Zhang M, Wang Y. Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies. Leg Med (Tokyo) 2018; 32:98-103. [PMID: 29626747 DOI: 10.1016/j.legalmed.2018.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 03/01/2018] [Accepted: 03/31/2018] [Indexed: 12/13/2022]
Abstract
Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.
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Affiliation(s)
- Shanshan Zhang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China
| | - Shuyi Han
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China.
| | - Maoxiu Zhang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China
| | - Yunshan Wang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China.
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Copy number variations of circulating, cell-free DNA in urothelial carcinoma of the bladder patients treated with radical cystectomy: a prospective study. Oncotarget 2017; 8:56398-56407. [PMID: 28915599 PMCID: PMC5593570 DOI: 10.18632/oncotarget.17657] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/26/2017] [Indexed: 12/18/2022] Open
Abstract
The aim of the present study was to establish a rapid profiling method using multiplex ligation-dependent probe amplification (MLPA) and characterize copy number variations (CNV) in circulating, cell-free DNA (cfDNA) in 85 urothelial carcinoma of the bladder (UCB) patients treated with radical cystectomy (RC). MLPA was tested for the use of cfDNA extracted from serum and plasma by various commercial extraction kits. Eighteen probes served as reference to control denaturation, ligation and amplification efficiency. MLPA was exclusively suitable for cfDNA extracted from serum. Serum from 72 patients (84.7%) could be analyzed. Thirty-five patients (48.6%) had presence of CNV in cfDNA. The median CNV count in patients with presence of CNV was 2. Predominantly, CNV were located in the genes CDH1, ZFHX3, RIPK2 and PTEN in 15 patients (20.8%), 12 patients (16.7%), 9 patients (12.5%) and 7 patients (9.7%), respectively. CNV in TSG1, RAD21, KIAA0196, ANXA7 and TMPRSS2 were associated with presence of variant UCB histology (p = 0.029, 0.029, 0.029, 0.029, 0.043, respectively). Furthermore, CNV in miR-15a, CDH1 and ZFHX3 were associated with presence of incidental prostate cancer (p = 0.023, 0.003, 0.025, respectively). Patients with CNV in KLF5, ZFHX3 and CDH1 had reduced cancer-specific survival, compared to patients without CNV in these genes (pairwise p = 0.028, 0.026, 0.044, respectively). MLPA represents an efficient method for the detection of CNV among numerous genes on various chromosomal regions. CNV in specific genes seem to be associated with aggressive UCB biologic features and presence of incidental prostate cancer, and may have a negative impact on cancer-specific survival.
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Breveglieri G, Travan A, D’Aversa E, Cosenza LC, Pellegatti P, Guerra G, Gambari R, Borgatti M. Postnatal and non-invasive prenatal detection of β-thalassemia mutations based on Taqman genotyping assays. PLoS One 2017; 12:e0172756. [PMID: 28235086 PMCID: PMC5325530 DOI: 10.1371/journal.pone.0172756] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/09/2017] [Indexed: 11/18/2022] Open
Abstract
The β-thalassemias are genetic disorder caused by more than 200 mutations in the β-globin gene, resulting in a total (β0) or partial (β+) deficit of the globin chain synthesis. The most frequent Mediterranean mutations for β-thalassemia are: β039, β+IVSI-110, β+IVSI-6 and β0IVSI-1. Several molecular techniques for the detection of point mutations have been developed based on the amplification of the DNA target by polymerase chain reaction (PCR), but they could be labor-intensive and technically demanding. On the contrary, TaqMan® genotyping assays are a simple, sensitive and versatile method suitable for the single nucleotide polymorphism (SNP) genotyping affecting the human β-globin gene. Four TaqMan® genotyping assays for the most common β-thalassemia mutations present in the Mediterranean area were designed and validated for the genotype characterization of genomic DNA extracted from 94 subjects comprising 25 healthy donors, 33 healthy carriers and 36 β-thalassemia patients. In addition, 15 specimens at late gestation (21–39 gestational weeks) and 11 at early gestation (5–18 gestational weeks) were collected from pregnant women, and circulating cell-free fetal DNAs were extracted and analyzed with these four genotyping assays. We developed four simple, inexpensive and versatile genotyping assays for the postnatal and prenatal identification of the thalassemia mutations β039, β+IVSI-110, β+IVSI-6, β0IVSI-1. These genotyping assays are able to detect paternally inherited point mutations in the fetus and could be efficiently employed for non-invasive prenatal diagnosis of β-globin gene mutations, starting from the 9th gestational week.
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Affiliation(s)
- Giulia Breveglieri
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
- Biotechnology Center, University of Ferrara, Ferrara, Italy
| | - Anna Travan
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
| | - Elisabetta D’Aversa
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
| | - Lucia Carmela Cosenza
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
- Biotechnology Center, University of Ferrara, Ferrara, Italy
| | - Patrizia Pellegatti
- Operative Unit of Laboratory Analysis, University Hospital S. Anna, Ferrara, Italy
| | - Giovanni Guerra
- Operative Unit of Laboratory Analysis, University Hospital S. Anna, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
- Biotechnology Center, University of Ferrara, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
- * E-mail:
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Silver RM, Myatt L, Hauth JC, Leveno KJ, Peaceman AM, Ramin SM, Samuels P, Saade G, Sorokin Y, Clifton RG, Reddy UM. Cell-Free Total and Fetal DNA in First Trimester Maternal Serum and Subsequent Development of Preeclampsia. Am J Perinatol 2017; 34:191-198. [PMID: 27398706 PMCID: PMC5358543 DOI: 10.1055/s-0035-1570383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Objective The objective of this study was to assess the relationship between first trimester cell-free total and fetal DNA in maternal plasma and the subsequent development of preeclampsia. Study Design Nested case-control study of patients enrolled in the Combined Antioxidant and Preeclampsia Prediction Studies prediction study of 175 women who did and 175 women who did not develop preeclampsia. The predictive values of cell-free total and fetal DNA and the subsequent development of preeclampsia were measured using receiver operating characteristic curves. Results Cell-free total DNA was higher in African American (median; 25-75%; 6.15; 0.14-28.73; p = 0.02) and Hispanic (4.95; 0.20-26.82; p = 0.037) compared with white women (2.33; 0.03-13.10). Levels of cell-free total DNA were also associated with maternal body mass index (BMI) (p = 0.02). Cell-free total DNA levels were similar between women who later developed preeclampsia (3.52; 0.11-25.3) and controls (3.74; 0.12-21.14, p = 0.96). Conclusion There is no significant difference in levels of cell-free total DNA in the first trimester in women who subsequently develop preeclampsia. Levels of cell-free total DNA in the first trimester are increased in African American and Hispanic compared with white women, and levels increase with increasing BMI.
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Affiliation(s)
- Robert M Silver
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Leslie Myatt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - John C Hauth
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Kenneth J Leveno
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Alan M Peaceman
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Susan M Ramin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Philip Samuels
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - George Saade
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Yoram Sorokin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Rebecca G Clifton
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Uma M Reddy
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
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de Haas M, Thurik FF, van der Ploeg CPB, Veldhuisen B, Hirschberg H, Soussan AA, Woortmeijer H, Abbink F, Page-Christiaens GCML, Scheffer PG, Ellen van der Schoot C. Sensitivity of fetal RHD screening for safe guidance of targeted anti-D immunoglobulin prophylaxis: prospective cohort study of a nationwide programme in the Netherlands. BMJ 2016; 355:i5789. [PMID: 27821701 PMCID: PMC5098549 DOI: 10.1136/bmj.i5789] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To determine the accuracy of non-invasive fetal testing for the RHD gene in week 27 of pregnancy as part of an antenatal screening programme to restrict anti-D immunoglobulin use to women carrying a child positive for RHD DESIGN: Prospectively monitoring of fetal RHD testing accuracy compared with serological cord blood typing on introduction of the test. Fetal RHD testing was performed with a duplex real time quantitative polymerase chain reaction, with cell-free fetal DNA isolated from 1 mL of maternal plasma The study period was between 4 July 2011 and 7 October 2012. The proportion of women participating in screening was determined. SETTING Nationwide screening programme, the Netherlands. Tests are performed in a centralised setting. PARTICIPANTS 25 789 RhD negative pregnant women. MAIN OUTCOME MEASURES Sensitivity, specificity, false negative rate, and false positive rate of fetal RHD testing compared with serological cord blood typing; proportion of technical failures; and compliance to the screening programme. RESULTS A fetal RHD test result and serological cord blood result were available for 25 789 pregnancies. Sensitivity for detection of fetal RHD was 99.94% (95% confidence interval 99.89% to 99.97%) and specificity was 97.74% (97.43% to 98.02%). Nine false negative results for fetal RHD testing were registered (0.03%, 95% confidence interval 0.01% to 0.06%). In two cases these were due to technical failures. False positive fetal RHD testing results were registered for 225 samples (0.87%, 0.76% to 0.99%). Weak RhD expression was shown in 22 of these cases, justifying anti-D immunoglobulin use. The negative and positive predictive values were 99.91% (95% confidence interval 99.82% to 99.95%) and 98.60% (98.40% to 98.77%), respectively. More than 98% of the women participated in the screening programme. CONCLUSIONS Fetal RHD testing in week 27 of pregnancy as part of a national antenatal screening programme is highly reliable and can be used to target both antenatal and postnatal anti-D immunoglobulin use.
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Affiliation(s)
- Masja de Haas
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Center for Clinical Transfusion Research, Sanquin Research and Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden
- Department of Immunohematology Diagnostic Services, Sanquin Research, Amsterdam, Netherlands
| | - Florentine F Thurik
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- University Medical Center Utrecht, Division Woman and Baby, Department of Obstetrics, Utrecht, Netherlands
| | | | - Barbera Veldhuisen
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Immunohematology Diagnostic Services, Sanquin Research, Amsterdam, Netherlands
| | - Hoang Hirschberg
- National Institute for Public Health and the Environment, Service for vaccine provision and prevention programs, Bilthoven, Netherlands
| | - Aicha Ait Soussan
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Heleen Woortmeijer
- Department of Immunohematology Diagnostic Services, Sanquin Research, Amsterdam, Netherlands
| | - Frithjofna Abbink
- National Institute for Public Health and the Environment, Center for population screening, Bilthoven, Netherlands
| | | | - Peter G Scheffer
- University Medical Center Utrecht, Division Woman and Baby, Department of Obstetrics, Utrecht, Netherlands
| | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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Breveglieri G, Gallo TE, Travan A, Pellegatti P, Guerra G, Gambari R, Borgatti M. Surface plasmon resonance analysis to detect the β +IVSI-110 thalassemia mutation in circulating cell-free fetal DNA. Clin Chim Acta 2016; 462:133-134. [PMID: 27642085 DOI: 10.1016/j.cca.2016.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Giulia Breveglieri
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy; Biotechnology Center, University of Ferrara, Ferrara, Italy
| | - Tiziana Eleonora Gallo
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
| | - Anna Travan
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy
| | - Patrizia Pellegatti
- Operative Unit of Laboratory Analysis, University Hospital S. Anna, Ferrara, Italy
| | - Giovanni Guerra
- Operative Unit of Laboratory Analysis, University Hospital S. Anna, Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy; Biotechnology Center, University of Ferrara, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, University of Ferrara, Ferrara, Italy.
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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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Moezzi L, Keshavarz Z, Ranjbaran R, Aboualizadeh F, Behzad-Behbahani A, Abdullahi M, Ramezani A, Samsami A, Sharifzadeh S. Fetal RHD Genotyping Using Real-Time Polymerase Chain Reaction Analysis of Cell-Free Fetal DNA in Pregnancy of RhD Negative Women in South of Iran. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2016; 10:62-70. [PMID: 27123202 PMCID: PMC4845531 DOI: 10.22074/ijfs.2016.4770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 06/29/2015] [Indexed: 11/04/2022]
Abstract
BACKGROUND Maternal-fetal RhD antigen incompatibility causes approximately 50% of clinically significant alloimmunization cases. The routine use of prophylactic anti-D immunoglobulin has dramatically reduced hemolytic disease of the fetus and newborn. Recently, fetal RHD genotyping in RhD negative pregnant women has been suggested for appropriate use of anti-D immunoglobulin antenatal prophylaxis and decrease unnecessary prenatal interventions. MATERIALS AND METHODS In this prospective cohort study, in order to develop a reliable and non-invasive method for fetal RHD genotyping, cell free fetal DNA (cffD- NA) was extracted from maternal plasma. Real-time quantitative polymerase chain reaction (qPCR) for detection of RHD exons 7, 5, 10 and intron 4 was performed and the results were compared to the serological results of cord blood cells as the gold standard method. SRY gene and hypermethylated Ras-association domain family member 1 (RASSF1A) gene were used to confirm the presence of fetal DNA in male and female fetuses, respectively. RESULTS Out of 48 fetuses between 8 and 32 weeks (wks) of gestational age (GA), we correctly diagnosed 45 cases (93.75%) of RHD positive fetuses and 2 cases (4.16%) of the RHD negative one. Exon 7 was amplified in one sample, while three other RHD gene sequences were not detected; the sample was classified as inconclusive, and the RhD serology result after birth showed that the fetus was RhD-negative. CONCLUSION Our results showed high accuracy of the qPCR method using cffDNA for fetal RHD genotyping and implicate on the efficiency of this technique to predict the competence of anti-D immunoglobulin administration.
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Affiliation(s)
- Leili Moezzi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Keshavarz
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Ranjbaran
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farzaneh Aboualizadeh
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Masooma Abdullahi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- School of Advanced Medical Science and Technology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alamtaj Samsami
- Department of Obstetrics and Gynecology, Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sedigheh Sharifzadeh
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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Breveglieri G, Bassi E, Carlassara S, Cosenza LC, Pellegatti P, Guerra G, Finotti A, Gambari R, Borgatti M. Y-chromosome identification in circulating cell-free fetal DNA using surface plasmon resonance. Prenat Diagn 2016; 36:353-61. [DOI: 10.1002/pd.4788] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/14/2015] [Accepted: 02/01/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Giulia Breveglieri
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section; University of Ferrara; Ferrara Italy
- Biotechnology Center; University of Ferrara; Ferrara Italy
| | - Elisabetta Bassi
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section; University of Ferrara; Ferrara Italy
| | - Silvia Carlassara
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section; University of Ferrara; Ferrara Italy
| | - Lucia Carmela Cosenza
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section; University of Ferrara; Ferrara Italy
- Biotechnology Center; University of Ferrara; Ferrara Italy
| | - Patrizia Pellegatti
- Operative Unit of Laboratory Analysis; University Hospital S. Anna; Ferrara Italy
| | - Giovanni Guerra
- Operative Unit of Laboratory Analysis; University Hospital S. Anna; Ferrara Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section; University of Ferrara; Ferrara Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section; University of Ferrara; Ferrara Italy
- Biotechnology Center; University of Ferrara; Ferrara Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section; University of Ferrara; Ferrara Italy
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Galbiati S, Monguzzi A, Damin F, Soriani N, Passiu M, Castellani C, Natacci F, Curcio C, Seia M, Lalatta F, Chiari M, Ferrari M, Cremonesi L. COLD-PCR and microarray: two independent highly sensitive approaches allowing the identification of fetal paternally inherited mutations in maternal plasma. J Med Genet 2016; 53:481-7. [PMID: 26912453 DOI: 10.1136/jmedgenet-2015-103229] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 02/03/2016] [Indexed: 11/03/2022]
Abstract
BACKGROUND Until now, non-invasive prenatal diagnosis of genetic diseases found only limited routine applications. In autosomal recessive diseases, it can be used to determine the carrier status of the fetus through the detection of a paternally inherited disease allele in cases where maternal and paternal mutated alleles differ. METHODS Conditions for non-invasive identification of fetal paternally inherited mutations in maternal plasma were developed by two independent approaches: coamplification at lower denaturation temperature-PCR (COLD-PCR) and highly sensitive microarrays. Assays were designed for identifying 14 mutations, 7 causing β-thalassaemia and 7 cystic fibrosis. RESULTS In total, 87 non-invasive prenatal diagnoses were performed by COLD-PCR in 75 couples at risk for β-thalassaemia and 12 for cystic fibrosis. First, to identify the more appropriate methodology for the analysis of minority mutated fetal alleles in maternal plasma, both fast and full COLD-PCR protocols were developed for the most common Italian β-thalassaemia Cd39 and IVSI.110 mutations. In 5 out of 31 samples, no enrichment was obtained with the fast protocol, while full COLD-PCR provided the correct fetal genotypes. Thus, full COLD-PCR protocols were developed for all the remaining mutations and all analyses confirmed the fetal genotypes obtained by invasive prenatal diagnosis. Microarray analysis was performed on 40 samples from 28 couples at risk for β-thalassaemia and 12 for cystic fibrosis. Results were in complete concordance with those obtained by both COLD-PCR and invasive procedures. CONCLUSIONS COLD-PCR and microarray approaches are not expensive, simple to handle, fast and can be easily set up in specialised clinical laboratories where prenatal diagnosis is routinely performed.
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Affiliation(s)
- Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Monguzzi
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Nadia Soriani
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marianna Passiu
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Carlo Castellani
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Federica Natacci
- Clinical Genetics Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristina Curcio
- Clinical Genetics Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Seia
- Clinical Genetics Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Faustina Lalatta
- Clinical Genetics Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy Università Vita-Salute San Raffaele, Milano, Italy
| | - Laura Cremonesi
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Ramezanzadeh M, Salehi M, Farajzadegan Z, Kamali S, Salehi R. Detection of paternally inherited fetal point mutations for β-thalassemia in maternal plasma using simple fetal DNA enrichment protocol with or without whole genome amplification: an accuracy assessment. J Matern Fetal Neonatal Med 2015; 29:2645-9. [PMID: 26553322 DOI: 10.3109/14767058.2015.1095883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To design and evaluate a noninvasive protocol for prenatal diagnosis (PND) of β-thalassemia, using cell free fetal DNA (cff-DNA) in maternal circulation. Traditional current PND which is mainly based on chorionic villous sampling (CVS), amplification refractory mutation system and sequencing holds as gold standard. METHODS Ten thalassemia trait couples with distinct mutations for the husband and wife were included in this study. The mutations in carrier fathers were IVSI-1, IVSI-5, FR8/9 and CD44. After maternal plasma isolation and free DNA extraction, all samples subjected to designed protocol including DNA size separation on agarose gel, elution of DNA from the gel slices using a simple and efficient manual purification method, with or without whole genome amplification and the detection method was allele-specific real-time PCR. RESULTS Presence or absence of the paternal mutant allele was correctly determined in all of cases and the accuracy of designed protocol was determined 100%. CONCLUSIONS The protocol described here is very simple, inexpensive and easy to perform, but with satisfactory accuracy in detection of paternal mutations in cff-DNA. Due to the risk of fetal loss with current invasive sampling for PND, a noninvasive alternative is highly demanded in clinical setting.
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Affiliation(s)
- Mahboubeh Ramezanzadeh
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan , Iran and
| | - Mansour Salehi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan , Iran and
| | - Ziba Farajzadegan
- b Department of Community Medicine , Isfahan University of Medical Sciences , Isfahan , Iran
| | - Sara Kamali
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan , Iran and
| | - Rasoul Salehi
- a Department of Genetics and Molecular Biology , School of Medicine, Isfahan University of Medical Sciences , Isfahan , Iran and
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Bronkhorst AJ, Aucamp J, Pretorius PJ. Cell-free DNA: Preanalytical variables. Clin Chim Acta 2015; 450:243-53. [DOI: 10.1016/j.cca.2015.08.028] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/17/2015] [Accepted: 08/30/2015] [Indexed: 12/11/2022]
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Jacob RR, Saxena R, Verma IC. Noninvasive Diagnosis of Fetal Gender: Utility of Combining DYS14 and SRY. Genet Test Mol Biomarkers 2015; 19:505-11. [PMID: 26121024 DOI: 10.1089/gtmb.2015.0040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Diagnosis of fetal gender early in pregnancy is very useful as it would prevent invasive fetal sampling in almost half the cases at risk of inheriting X-linked disorders or those affecting sexual differentiation. Noninvasive prenatal diagnosis (NIPD) using circulating cell-free fetal (cff) DNA from maternal circulation has emerged as a useful alternative to existing methods for prenatal diagnosis of gender. NIPD eliminates the risk of miscarriage from invasive prenatal diagnosis and the necessity of possessing specialized obstetric skills for fetal tissue sampling. The aim of this study was to compare two Y chromosome markers-SRY and DYS14-for their utility in the diagnosis of fetal gender. SUBJECTS AND METHODS Forty-eight plasma samples from pregnant women between 9 and 25 weeks of gestation were analyzed. Real-time polymerase chain reaction was performed on cff DNA extracted from maternal plasma to detect fetal Y chromosome with SRY (n=27) and DYS14 (n=48) markers. RESULTS We observed 100% sensitivity and 85.6% specificity in noninvasive Y chromosome detection with the combined use of DYS14 and SRY markers (n=27) compared with the results obtained on using DYS14 (n=48 sensitivity 94%; specificity 71.4%) and SRY (n=27, sensitivity 84%; specificity 92.8%) markers alone. CONCLUSION Our results show that the test performance improved with the employment of two Y-amplification assays.
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Affiliation(s)
| | - Renu Saxena
- Centre of Medical Genetics, Sir Ganga Ram Hospital , New Delhi, India
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Frickmann H, Hinz R, Hagen RM. Comparison of an automated nucleic acid extraction system with the column-based procedure. Eur J Microbiol Immunol (Bp) 2015; 5:94-102. [PMID: 25883797 DOI: 10.1556/eujmi-d-14-00040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 12/23/2014] [Indexed: 12/21/2022] Open
Abstract
Here, we assessed the extraction efficiency of a deployable bench-top nucleic acid extractor EZ1 in comparison to the column-based approach with complex sample matrices. A total of 48 EDTA blood samples and 81 stool samples were extracted by EZ1 automated extraction and the column-based QIAamp DNA Mini Kit. Blood sample extractions were assessed by two real-time malaria PCRs, while stool samples were analyzed by six multiplex real-time PCR assays targeting bacterial, viral, and parasitic stool pathogens. Inhibition control PCR testing was performed as well. In total, 147 concordant and 13 discordant pathogen-specific PCR results were obtained. The latter comprised 11 positive results after column-based extraction only and two positive results after EZ1 extraction only. EZ1 extraction showed a higher frequency of inhibition. This phenomenon was, however, inconsistent for the different PCR schemes. In case of concordant PCR results, relevant differences of cycle threshold numbers for the compared extraction schemes were not observed. Switches from well-established column-based extraction to extraction with the automated EZ1 system do not lead to a relevantly reduced yield of target DNA when complex sample matrices are used. If sample inhibition is observed, column-based extraction from another sample aliquot may be considered.
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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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Picchiassi E, Di Renzo GC, Tarquini F, Bini V, Centra M, Pennacchi L, Galeone F, Micanti M, Coata G. Non-Invasive Prenatal RHD Genotyping Using Cell-Free Fetal DNA from Maternal Plasma: An Italian Experience. Transfus Med Hemother 2014; 42:22-8. [PMID: 25960712 DOI: 10.1159/000370233] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/27/2014] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND This study assessed the diagnostic accuracy of a non-invasive approach to fetal RHD genotyping using cell-free fetal DNA in maternal plasma and a combination of methodological strategies. METHODS Real-time PCR (qPCR) was performed on 216 RhD-negative women between weeks 10+0 and 14+6 of gestation (1st qPCR). qPCR was repeated (2nd qPCR) to increase the amount of each sample for analysis, on 95 plasma aliquots that were available from first trimester blood collection (group 1) and on 13 samples that were collected between weeks 18+0 and 25+6 of gestation (group 2). qPCR was specific for exons 5 and 7 of the RHD gene (RHD5 and RHD7). The results were interpreted according to the number of positive replicates of both exons. RESULTS 1st qPCR: diagnostic accuracy was of 93.3%. Diagnostic accuracy increased from 90.5% (1st qPCR) to 93.7% (2nd qPCR) in group 1 and from 84.6% (1st qPCR) to 92.3% (2nd qPCR) in group 2. These increments were not statistically significant. CONCLUSION Our approach to RHD genotyping in early pregnancy yielded high diagnostic accuracy. Increasing the amount of DNA analyzed in each sample did not improve significantly the diagnostic accuracy of the test.
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Affiliation(s)
- Elena Picchiassi
- Department of Obstetrics and Gynecology, University Hospital of Perugia, Perugia, Italy
| | - Gian Carlo Di Renzo
- Department of Obstetrics and Gynecology, University Hospital of Perugia, Perugia, Italy
| | - Federica Tarquini
- Department of Obstetrics and Gynecology, University Hospital of Perugia, Perugia, Italy
| | - Vittorio Bini
- Department of Internal Medicine, University Hospital of Perugia, Perugia, Italy
| | - Michela Centra
- Department of Obstetrics and Gynecology, University Hospital of Perugia, Perugia, Italy
| | - Luana Pennacchi
- Department of Obstetrics and Gynecology, University Hospital of Perugia, Perugia, Italy
| | - Fabiana Galeone
- Department of Obstetrics and Gynecology, University Hospital of Perugia, Perugia, Italy
| | - Mara Micanti
- Department of Obstetrics and Gynecology, University Hospital of Perugia, Perugia, Italy
| | - Giuliana Coata
- Department of Obstetrics and Gynecology, University Hospital of Perugia, Perugia, Italy
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Repiská G, Sedláčková T, Szemes T, Minárik G. Effect of different DNA concentration methods on performance of non-invasive fetal y-chromosomal short tandem repeat profiling from maternal plasma. Fetal Diagn Ther 2014; 37:58-64. [PMID: 25096632 DOI: 10.1159/000362664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND The accuracy and reliability of detection of free fetal DNA in plasma of pregnant women can be significantly improved by increasing the overall DNA concentration following the isolation from maternal plasma. The aim of our study was to compare DNA concentration methods on samples with free fetal DNA. MATERIALS AND METHODS DNA isolated from plasma samples of pregnant women carrying a male fetus were concentrated by 3 different methods: vacuum concentration, centrifugal filters and spin columns. Their performance was evaluated using PCR-based Y-chromosomal short tandem repeat (Y-STR) genotyping of the fetus. RESULTS A statistically significant difference was found between the 3 tested methods (F = 15.57, p < 0.0001). Using vacuum concentration 85.3% of paternally inherited Y-STR alleles were correctly identified. A significantly smaller proportion of alleles was correctly identified in samples concentrated by centrifugal filters and spin columns - 75.9 and 66.5%, respectively. DISCUSSION The highest proportion of paternally inherited Y-STR alleles was found in samples concentrated with the use of vacuum concentration. This concentration procedure does not require further handling of the sample either, which is an advantage because it avoids potential sample contamination. On the other hand, when automation is considered, vacuum concentration is less suitable because of an uneven and unpredictable sample evaporation rate. © 2014 S. Karger AG, Basel.
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Affiliation(s)
- Gabriela Repiská
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, and Geneton Ltd., Bratislava, Slovakia
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Devonshire AS, Whale AS, Gutteridge A, Jones G, Cowen S, Foy CA, Huggett JF. Towards standardisation of cell-free DNA measurement in plasma: controls for extraction efficiency, fragment size bias and quantification. Anal Bioanal Chem 2014; 406:6499-512. [PMID: 24853859 PMCID: PMC4182654 DOI: 10.1007/s00216-014-7835-3] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/26/2014] [Accepted: 04/14/2014] [Indexed: 01/01/2023]
Abstract
Circulating cell-free DNA (cfDNA) is becoming an important clinical analyte for prenatal testing, cancer diagnosis and cancer monitoring. The extraction stage is critical in ensuring clinical sensitivity of analytical methods measuring minority nucleic acid fractions, such as foetal-derived sequences in predominantly maternal cfDNA. Consequently, quality controls are required for measurement of extraction efficiency, fragment size bias and yield for validation of cfDNA methods. We evaluated the utility of an external DNA spike for monitoring these parameters in a study comparing three specific cfDNA extraction methods [QIAamp® circulating nucleic acid (CNA) kit, NucleoSpin® Plasma XS (NS) kit and FitAmp™ plasma/serum DNA isolation (FA) kit] with the commonly used QIAamp DNA blood mini (DBM) kit. We found that the extraction efficiencies of the kits ranked in the order CNA kit > DBM kit > NS kit > FA kit, and the CNA and NS kits gave a better representation of smaller DNA fragments in the extract than the DBM kit. We investigated means of improved reporting of cfDNA yield by comparing quantitative PCR measurements of seven different reference gene assays in plasma samples and validating these with digital PCR. We noted that the cfDNA quantities based on measurement of some target genes (e.g. TERT) were, on average, more than twofold higher than those of other assays (e.g. ERV3). We conclude that analysis and averaging of multiple reference genes using a GeNorm approach gives a more reliable estimate of total cfDNA quantity. Comparison of single and multiple reference gene normalisation for quantification of plasma cell free DNA ![]()
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Affiliation(s)
- Alison S Devonshire
- Molecular and Cell Biology Team, LGC Ltd, Queen's Road, Teddington, TW11 0LY, UK,
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Repiská G, Sedláčková T, Szemes T, Celec P, Minárik G. Selection of the optimal manual method of cell free fetal DNA isolation from maternal plasma. Clin Chem Lab Med 2014; 51:1185-9. [PMID: 23241606 DOI: 10.1515/cclm-2012-0418] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 11/07/2012] [Indexed: 11/15/2022]
Abstract
BACKGROUND The cell free fetal DNA (cffDNA) present in plasma of pregnant women represents an important alternative source of DNA for non-invasive prenatal diagnosis. Due to the low quantity and increased fragmentation of cffDNA, the choice of DNA extraction method is a crucial step for downstream analyses. METHODS In our study, the three spin column-based kits for isolation of cffDNA [DNA Blood Mini Kit (DBM), DSP Virus Kit (DSP) and Circulating Nucleic Acid (CNA) Kit] were compared. Original and optimized protocol were used in comparison and applied in the two phases of the study. RESULTS A statistically significant difference in performance of the kits was determined based on the comparison of genomic equivalents per mL (GEq/mL) values (p<0.0001). The GEq/mL of isolated DNA was significantly higher using CNA and DSP Kits than DBM Kit. The CNA Kit and DSP Kit did not significantly differ in the GEq/mL values, although all tested samples isolated with CNA Kit showed higher values. CONCLUSIONS According to our results the commonly used DBM Kit could be successfully replaced with CNA or DSP Kits. The replacement could be beneficial in qualitative as well quantitative tests (e.g., gender determination, aneuploidy detection) when the isolation yield limits subsequent analyses. However, there is an important decision to be made when switching DBM Kit for DSP or CNA Kits. The price of DBM Kit is two and six times lower than DSP and CNA Kits, respectively.
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Affiliation(s)
- Gabriela Repiská
- Comenius University in Bratislava Faculty of Medicine, Institute of Molecular Biomedicine, Bratislava, Slovakia.
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Abstract
In this study, we assessed the feasibility of fetal RhD genotyping by analysis of cell-free fetal DNA(cffDNA) extracted from plasma samples of Rhesus (Rh) D-negative pregnant women by using real-time polymerase chain reaction (PCR). Fetal genotyping was performed on 30 RhD-negative women between 9 and 39 weeks of gestation who were referred to us for invasive testing [amniocentesis/chorionic villi sampling (CVS)]. The fetal RHD genotype was determined based on real-time PCR method. Exons 7 and 10 of the RHD and SRY genes were targeted. Among the pregnant women, 12 were carrying male and 17 were carrying female fetuses. Out of 29 pregnant women, 21 had RhD-positive and nine had RhD-negative fetuses. One sample (case 12, whose blood group was found to be AB Rh [+]) was excluded due to controversial results from repeated serological analyses. All prenatal results were in concordance with postnatal RhD status and fetal sex without false- positive or -negative results. Performing real-time PCR on cffDNA showed accurate, efficient and reliable results, allowing rapid and high throughput non invasive determination of fetal sex and RhD status in clinical samples.
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Ou X, Wang H, Qu D, Chen Y, Gao J, Sun H. Epigenome-wide DNA methylation assay reveals placental epigenetic markers for noninvasive fetal single-nucleotide polymorphism genotyping in maternal plasma. Transfusion 2014; 54:2523-33. [PMID: 24749853 DOI: 10.1111/trf.12659] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/14/2014] [Accepted: 02/19/2014] [Indexed: 01/03/2023]
Abstract
BACKGROUND The use of DNA methylation difference between maternal blood cell and fetal (placental) DNA is one of the main areas of interest for the development of fetal epigenetics markers in maternal plasma. STUDY DESIGN AND METHODS We employed a methylation array (HumanMethylation450 array, Illumina, Inc.) to identify novel biomarkers that are specially hypermethylated in placental DNA versus maternal blood cells in a genome-wide basis. Validation by bisulfite genomic sequencing was performed and the priority was given to potential targets that harbor differential methylated CpG sites overlapped with at least two methylation-sensitive restriction enzyme (MSRE) recognizing sites, as well as one polymorphic single-nucleotide polymorphism (SNP), within a short DNA stretch. Three candidate regions of PSMB8, SKI, and CHST11 gene were selected for developing a preliminary polymerase chain reaction assay with MSRE digestion of maternal plasma DNA. SNP genotypes were confirmed by direct sequencing. RESULTS We identified 2944 and 5218 fetal-specific hypermethylated CpG sites in the first- and third-trimester placenta, respectively, of which 2613 were overlapped, suggesting a consistency of differential methylation during the whole pregnancy. The array results were confirmed by bisulfite genomic sequencing. The preliminary tests in maternal plasma showed that postdigestion hypermathylated versions of these candidate molecules were detectable only in pregnant women. We further revealed that methylated targets in maternal plasma possessed the fetal SNP genotypes. CONCLUSION The present studies systematically identified hypermethylated sites in fetal tissues and preliminarily demonstrated that some of the fetal epigenetic markers that contain informative SNPs have great potential for noninvasive fetal genetic diagnosis.
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Affiliation(s)
- Xueling Ou
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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Clausen FB. Integration of noninvasive prenatal prediction of fetal blood group into clinical prenatal care. Prenat Diagn 2014; 34:409-15. [PMID: 24431264 DOI: 10.1002/pd.4326] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/08/2014] [Accepted: 01/12/2014] [Indexed: 12/21/2022]
Abstract
Incompatibility of red blood cell blood group antigens between a pregnant woman and her fetus can cause maternal immunization and, consequently, hemolytic disease of the fetus and newborn. Noninvasive prenatal testing of cell-free fetal DNA can be used to assess the risk of hemolytic disease of the fetus and newborn to fetuses of immunized women. Prediction of the fetal RhD type has been very successful and is now integrated into clinical practice to assist in the management of the pregnancies of RhD immunized women. In addition, noninvasive prediction of the fetal RhD type can be applied to guide targeted prenatal prophylaxis, thus avoiding unnecessary exposure to anti-D in pregnant women. The analytical aspect of noninvasive fetal RHD typing is very robust and accurate, and its routine utilization has demonstrated high sensitivities for fetal RHD detection. A high compliance with administering anti-D is essential for obtaining a clinical effect. Noninvasive fetal typing of RHC/c, RHE/e, and KEL may become more widely used in the future.
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Affiliation(s)
- Frederik Banch Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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de Haas M, Finning K, Massey E, Roberts DJ. Anti-D prophylaxis: past, present and future. Transfus Med 2014; 24:1-7. [DOI: 10.1111/tme.12099] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- M. de Haas
- Department of Immunohaematology, Division of Diagnostic Services; Sanquin; Amsterdam the Netherlands
| | - K. Finning
- National Health Service Blood and Transplant; Bristol UK
| | - E. Massey
- National Health Service Blood and Transplant; Bristol UK
| | - D. J. Roberts
- National Health Service Blood and Transplant; Oxford UK
- Radcliffe Department of Medicine, John Radcliffe Hospital; University of Oxford; Oxford UK
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Kolialexi A, Tounta G, Mavrou A. Noninvasive fetal RhD genotyping from maternal blood. Expert Rev Mol Diagn 2014; 10:285-96. [DOI: 10.1586/erm.10.5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Pre-analytical conditions in non-invasive prenatal testing of cell-free fetal RHD. PLoS One 2013; 8:e76990. [PMID: 24204719 PMCID: PMC3800077 DOI: 10.1371/journal.pone.0076990] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/26/2013] [Indexed: 02/03/2023] Open
Abstract
Background Non-invasive prenatal testing of cell-free fetal DNA (cffDNA) in maternal plasma can predict the fetal RhD type in D negative pregnant women. In Denmark, routine antenatal screening for the fetal RhD gene (RHD) directs the administration of antenatal anti-D prophylaxis only to women who carry an RhD positive fetus. Prophylaxis reduces the risk of immunization that may lead to hemolytic disease of the fetus and the newborn. The reliability of predicting the fetal RhD type depends on pre-analytical factors and assay sensitivity. We evaluated the testing setup in the Capital Region of Denmark, based on data from routine antenatal RHD screening. Methods Blood samples were drawn at gestational age 25 weeks. DNA extracted from 1 mL of plasma was analyzed for fetal RHD using a duplex method for exon 7/10. We investigated the effect of blood sample transportation time (n = 110) and ambient outdoor temperatures (n = 1539) on the levels of cffDNA and total DNA. We compared two different quantification methods, the delta Ct method and a universal standard curve. PCR pipetting was compared on two systems (n = 104). Results The cffDNA level was unaffected by blood sample transportation for up to 9 days and by ambient outdoor temperatures ranging from -10°C to 28°C during transport. The universal standard curve was applicable for cffDNA quantification. Identical levels of cffDNA were observed using the two automated PCR pipetting systems. We detected a mean of 100 fetal DNA copies/mL at a median gestational age of 25 weeks (range 10–39, n = 1317). Conclusion The setup for real-time PCR-based, non-invasive prenatal testing of cffDNA in the Capital Region of Denmark is very robust. Our findings regarding the transportation of blood samples demonstrate the high stability of cffDNA. The applicability of a universal standard curve facilitates easy cffDNA quantification.
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Evaluation of sample stability and automated DNA extraction for fetal sex determination using cell-free fetal DNA in maternal plasma. BIOMED RESEARCH INTERNATIONAL 2013; 2013:195363. [PMID: 24222898 PMCID: PMC3814069 DOI: 10.1155/2013/195363] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 08/24/2013] [Accepted: 09/16/2013] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The detection of paternally inherited sequences in maternal plasma, such as the SRY gene for fetal sexing or RHD for fetal blood group genotyping, is becoming part of daily routine in diagnostic laboratories. Due to the low percentage of fetal DNA, it is crucial to ensure sample stability and the efficiency of DNA extraction. We evaluated blood stability at 4°C for at least 24 hours and automated DNA extraction, for fetal sex determination in maternal plasma. METHODS A total of 158 blood samples were collected, using EDTA-K tubes, from women in their 1st trimester of pregnancy. Samples were kept at 4°C for at least 24 hours before processing. An automated DNA extraction was evaluated, and its efficiency was compared with a standard manual procedure. The SRY marker was used to quantify cfDNA by real-time PCR. RESULTS Although lower cfDNA amounts were obtained by automated DNA extraction (mean 107,35 GE/mL versus 259,43 GE/mL), the SRY sequence was successfully detected in all 108 samples from pregnancies with male fetuses. CONCLUSION We successfully evaluated the suitability of standard blood tubes for the collection of maternal blood and assessed samples to be suitable for analysis at least 24 hours later. This would allow shipping to a central reference laboratory almost from anywhere in Europe.
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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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Gahan PB. Circulating nucleic acids in plasma and serum: applications in diagnostic techniques for noninvasive prenatal diagnosis. Int J Womens Health 2013; 5:177-86. [PMID: 23637563 PMCID: PMC3634397 DOI: 10.2147/ijwh.s34442] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The analysis of fetal nucleic acids in maternal blood 13 years ago has led to the initiation of noninvasive methods for the early determination of fetal gender, rhesus D status, and a number of aneuploid disorders and hemoglobinopathies. Subsequently, a comparatively large quantity of fetal DNA and RNA has been demonstrated in amniotic fluid as well as small amounts in premature infant saliva. The DNA and RNA in amniotic fluid has permitted an analysis of core transcriptomes, whilst the DNA and RNA in saliva allows the early detection and treatment monitoring of fetal developmental problems. These aspects are discussed together with the methodology and limits of analysis for noninvasive prenatal diagnosis in predictive, preventive, and personalized medicine.
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Affiliation(s)
- Peter B Gahan
- Anatomy and Human Sciences Department, King’s College London, London Bridge, London, UK
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Ordoñez E, Rueda L, Cañadas MP, Fuster C, Cirigliano V. Development and validation of multiplex real-time PCR assay for noninvasive prenatal assessment of fetal RhD status and fetal sex in maternal plasma. Fetal Diagn Ther 2013; 34:13-8. [PMID: 23548569 DOI: 10.1159/000346809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 01/04/2013] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Noninvasive prenatal detection of RhD status and fetal sex is becoming part of daily practice in clinical laboratories. We evaluated a high throughput procedure for automated DNA extraction and developed a multiplex real-time PCR (rt-PCR) for the simultaneous detection of three fetal loci in a single reaction to assess fetal sex and RhD status in maternal plasma. METHODS An automated DNA extraction method was evaluated together with a new multiplex rt-PCR assay for the simultaneous detection of exons 5 and 7 of the RHD gene together with the Y chromosome marker DYS14 in maternal plasma. The test was evaluated on 60 samples of known fetal genotype obtained from RhD-negative pregnant women before being applied prospectively on 158 consecutive clinical cases. Results were compared with newborn phenotypes. RESULTS Automated DNA extraction allowed successful analysis of all samples. DYS14 was detected in 118 cases (male fetuses) and both RHD exon 5 and 7 were detected in 148 samples. In 70 samples neither RHD exon 5 nor RHD exon 7 were detected (RhD-negative fetuses). Absence of all three sequences (female RhD-negative fetuses) was assessed in 33 samples. All prenatal results were in concordance with postnatal RhD status and fetal sex without false- positive or -negative results. CONCLUSION The automated DNA extraction procedure coupled with a novel multiplex rt-PCR assay proved accurate, efficient and reliable allowing rapid and high throughput noninvasive determination of fetal sex and RhD status in clinical samples.
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Affiliation(s)
- Elena Ordoñez
- Departament de Genètica Molecular, Labco Diagnostics, Barcelona, Spain
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Dovč-Drnovšek T, Klemenc P, Toplak N, Blejec T, Bricl I, Rožman P. Reliable Determination of Fetal RhD Status by RHD Genotyping from Maternal Plasma. ACTA ACUST UNITED AC 2013; 40:37-43. [PMID: 23637648 DOI: 10.1159/000345682] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Accepted: 04/12/2012] [Indexed: 02/04/2023]
Abstract
BACKGROUND Immunoprophylaxis with IgG anti-D is a standard prevention of hemolytic disease of the fetus and newborn. Fetal Rhesus D (RhD) blood group genotyping from maternal plasma of RhD-negative pregnant women allows targeted prophylaxis with IgG anti-D in RhD-positive pregnancies only. We set up a reliable protocol for prenatal RHD genotyping. METHODS 153 pregnant Caucasian RhD-negative women were tested in the 27th week (range 7-38th week) of pregnancy. 18 of them were alloimmunized to the RhD antigen. The fetal RHD genotype was determined based on an automated DNA extraction and real-time polymerase chain reaction method. Intron 4 and exons 5, 7 and 10 of the RHD gene and the SRY gene were targeted. RESULTS The fetal RhD status and gender was 100% correctly predicted in all 153 pregnancies (55 RhD-positive males, 45 RhD-positive females; 23 RhD-negative males, 30 RhD-negative females). CONCLUSION The accuracy and applicability of our protocol for non-invasive fetal RhD determination allows the correct management of RhD-incompatible pregnancies. Our protocol could prevent unnecessary immunoprophylaxis in 53 of 153 cases. We therefore recommend that non-invasive fetal RHD genotyping is introduced as an obligatory part of prenatal screening.
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Affiliation(s)
- Tadeja Dovč-Drnovšek
- Blood Transfusion Center of Slovenia, University Medical Center, Ljubljana, Slovenia
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Cell-free fetal DNA and adverse outcome in low risk pregnancies. Eur J Obstet Gynecol Reprod Biol 2012; 166:10-3. [PMID: 23021026 DOI: 10.1016/j.ejogrb.2012.09.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 08/05/2012] [Accepted: 09/03/2012] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To analyze in a large prospective cohort study of low risk pregnancies whether cell-free fetal (cff) DNA in maternal plasma of the second trimester might be associated with the development of preeclampsia, preterm delivery, and small for gestational age. STUDY DESIGN A subset of a large prospective cohort study in serological RhD negative pregnant women with RHD positive fetuses was used. Cff DNA was determined through the detection of RHD specific sequences with real-time PCR. RESULTS In 611 pregnancies, rates of 7.2% preeclampsia, 1.6% preterm birth ≤32, 2.9% ≤34, and 12.4% ≤37 weeks of gestation, 5.7% of small for gestational age <5th percentile, and 8.2% <10th percentile were observed. For none of these risk groups an association with cff DNA could be established. CONCLUSION Cff DNA in maternal plasma of the second trimester was not found to be a marker for an adverse pregnancy outcome in low risk pregnancies.
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Moussa H, Tsochandaridis M, Chakroun T, Jridi S, Abdelneji B, Hmida S, Silvy M, Bailly P, Gabert J, Levy-Mozziconacci A, Jemni-Yacoub S. Molecular background of D-negative phenotype in the Tunisian population. Transfus Med 2012; 22:192-8. [PMID: 22420413 DOI: 10.1111/j.1365-3148.2012.01142.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Most studies of the molecular basis of Rhesus D-negative phenotype have been conducted in Caucasian and African populations. A comprehensive survey of RHD alleles was lacking in people from North Africa (Tunisians, Moroccans and Algerians) which could be very efficient for managing donors and patients carrying an RHD molecular variant. We analyse the molecular background of D-negative population in Tunisia in the present study. MATERIALS AND METHODS Blood samples were collected from native Tunisians. A total of 448 D-negative donors from different regions of Tunisia were analysed by RHD genotyping according to an adopted strategy using real-time PCR, ASP-PCR and sequencing. RESULTS Among the 448 D-negative samples, 443 were phenotyped unequivocally as true D-negative including three molecular backgrounds which were RHD gene deletion (n = 437), RHDψ pseudogene (n = 2) and RHD-CE-D hybrid gene (n = 4) with the respective frequencies of 0·9900, 0·0023 and 0·0046. The remaining five samples, in discordance with the serological results, were identified as two weak D type 11, one weak D type 29, one weak D type 4·0 and one DBT-1 partial D. CONCLUSION This study showed that the Tunisian population gets closer to Caucasians, given that the RHD gene deletion is the most prevalent cause of D-negative phenotype, but it is slightly different by the presence of the RHDψ pseudogene which was found with a very low frequency compared with that described in the African population. Nevertheless, the relative occurrence of weak D variants among studied serologically D-negative samples make necessary the adaptation of RHD genotyping strategy to the spectrum of prevalent alleles.
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Affiliation(s)
- H Moussa
- Unité de Recherche UR06SP05 Centre Régional de Transfusion Sanguine, Sousse, Tunisia
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Cardo L, Prieto B, Álvarez FV. Noninvasive fetal RHD genotyping in the first trimester of pregnancy. Prenat Diagn 2012; 32:99. [DOI: 10.1002/pd.2851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Leyre Cardo
- Laboratorio de Medicina; Hospital Universitario Central de Asturias; Asturias Spain
| | - Belén Prieto
- Laboratorio de Medicina; Hospital Universitario Central de Asturias; Asturias Spain
| | - Francisco V. Álvarez
- Laboratorio de Medicina; Hospital Universitario Central de Asturias; Asturias Spain
- Departamento de Bioquímica y Biología Molecular; Universidad de Oviedo; Asturias Spain
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Noninvasive fetal sex determination in maternal plasma: a prospective feasibility study. Genet Med 2012; 14:101-6. [DOI: 10.1038/gim.2011.8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Lim JH, Kim SY, Park SY, Lee SY, Kim MJ, Han YJ, Lee SW, Chung JH, Kim MY, Yang JH, Ryu HM. Non-invasive epigenetic detection of fetal trisomy 21 in first trimester maternal plasma. PLoS One 2011; 6:e27709. [PMID: 22132128 PMCID: PMC3223183 DOI: 10.1371/journal.pone.0027709] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 10/23/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Down syndrome (DS) is the most common known aneuploidy, caused by an extra copy of all or part of chromosome 21. Fetal-specific epigenetic markers have been investigated for non-invasive prenatal detection of fetal DS. The phosphodiesterases gene, PDE9A, located on chromosome 21q22.3, is completely methylated in blood (M-PDE9A) and unmethylated in the placenta (U-PDE9A). Therefore, we estimated the accuracy of non-invasive fetal DS detection during the first trimester of pregnancy using this tissue-specific epigenetic characteristic of PDE9A. METHODOLOGY/PRINCIPAL FINDINGS A nested, case-control study was conducted using maternal plasma samples collected from 108 pregnant women carrying 18 DS and 90 normal fetuses (each case was matched with 5 controls according to gestational weeks at blood sampling). All pregnancies were singletons at or before 12 weeks of gestation between October 2008 and May 2009. The maternal plasma levels of M-PDE9A and U-PDE9A were measured by quantitative methylation-specific polymerase chain reaction. M-PDE9A and U-PDE9A levels were obtained in all samples and did not differ between male and female fetuses. M-PDE9A levels did not differ between the DS cases and controls (1854.3 vs 2004.5 copies/mL; P = 0.928). U-PDE9A levels were significantly elevated in women with DS fetuses compared with controls (356.8 vs 194.7 copies/mL, P<0.001). The sensitivities of U-PDE9A level and the unmethylation index of PDE9A for non-invasive fetal DS detection were 77.8% and 83.3%, respectively, with a 5% false-positive rate. In the risk assessment for fetal DS, the adjusted odds ratios of U-PDE9A level and UI were 46.2 [95% confidence interval: 7.8-151.6] and 63.7 [95% confidence interval: 23.2-206.7], respectively. CONCLUSIONS Our findings suggest that U-PDE9A level and the unmethylation index of PDE9A may be useful biomarkers for non-invasive fetal DS detection during the first trimester of pregnancy, regardless of fetal gender.
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Affiliation(s)
- Ji Hyae Lim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | - Shin Young Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | - So Yeon Park
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | - Shin Yeong Lee
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | - Mi Jin Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | - You Jung Han
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, KwanDong University college of Medicine, Seoul, Korea
| | - Si Won Lee
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, KwanDong University college of Medicine, Seoul, Korea
| | - Jin Hoon Chung
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, KwanDong University college of Medicine, Seoul, Korea
| | - Moon Young Kim
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, KwanDong University college of Medicine, Seoul, Korea
| | - Jae Hyug Yang
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, KwanDong University college of Medicine, Seoul, Korea
| | - Hyun Mee Ryu
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, KwanDong University college of Medicine, Seoul, Korea
- * E-mail:
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The controversy about controls for fetal blood group genotyping by cell-free fetal DNA in maternal plasma. Curr Opin Hematol 2011; 18:467-73. [DOI: 10.1097/moh.0b013e32834bab2d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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