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Kho SL, Chua KH, George E, Tan JAMA. A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β°-thalassaemia deletion. Sci Rep 2015; 5:13937. [PMID: 26365497 PMCID: PMC4568469 DOI: 10.1038/srep13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/31/2015] [Indexed: 11/11/2022] Open
Abstract
Homozygosity for the α-thalassaemia Southeast Asian (α-SEA) and Filipino β0-thalassaemia (β-FIL) deletions can cause serious complications leading to foetal death or life-long blood transfusions. A rapid and accurate molecular detection assay is essential in populations where the deletions are common. In this study, gap-polymerase chain reaction (PCR) with high resolution melting (HRM) analysis was developed to detect both the large deletions. Melting curves at 86.9 ± 0.1 °C were generated by normal individuals without the α-SEA deletion, 84.7 ± 0.1 °C by homozygous α-SEA deletion individuals and two melting curves at 84.7 ± 0.1 °C and 86.9 ± 0.1 °C by α-SEA deletion carriers. Normal individuals without the β-FIL deletion produce amplicons with a melting temperature (Tm) at 74.6 ± 0.1 °C, homozygous β-FIL individuals produce amplicons with Tm at 73.6 ± 0.1 °C and heterozygous β-FIL individuals generate two amplicons with Tm at 73.6 ± 0.1 °C and 74.6 ± 0.1 °C. Evaluation using blinded tests on 220 DNA samples showed 100% sensitivity and specificity. The developed assays are sensitive and specific for rapid molecular and prenatal diagnosis for the α-SEA and β-FIL deletions.
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Affiliation(s)
- Siew Leng Kho
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Jin Ai Mary Anne Tan
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Yi L, Huang Y, Wu T, Wu J. A magnetic nanoparticles-based method for DNA extraction from the saliva of stroke patients. Neural Regen Res 2013; 8:3036-46. [PMID: 25206624 PMCID: PMC4146207 DOI: 10.3969/j.issn.1673-5374.2013.32.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022] Open
Abstract
C677T polymorphism in the methylenetetrahydrofolate reductase (MTHFR) gene is a risk factor for stroke, suggesting that widespread detection could help to prevent stroke. DNA from 70 stroke patients and 70 healthy controls was extracted from saliva using a magnetic nanoparticles-based method and from blood using conventional methods. Real-time PCR results revealed that the C677T polymorphism was genotyped by PCR using DNA extracted from both saliva and blood samples. The genotype results were confirmed by gene sequencing, and results for saliva and blood samples were consistent. The mutation TT genotype frequency was significantly higher in the stroke group than in controls. Homocysteine levels were significantly higher than controls in both TT genotype groups. Therefore, this noninvasive magnetic nanoparticles-based method using saliva samples could be used to screen for the MTHFR C677T polymorphism in target populations.
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Affiliation(s)
- Li Yi
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Ying Huang
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Ting Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
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Traeger-Synodinos J, Vrettou C, Kanavakis E. Prenatal, noninvasive and preimplantation genetic diagnosis of inherited disorders: hemoglobinopathies. Expert Rev Mol Diagn 2011; 11:299-312. [PMID: 21463239 DOI: 10.1586/erm.11.7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Disorders of hemoglobin synthesis have been used as a prototype for the development of most approaches for prenatal diagnosis (PND). PND for hemoglobinopathies based on molecular analysis of trophoblast or amniocyte DNA has accumulated approximately 30 years of experience. Disadvantages with conventional PND include 'invasive' fetal sampling and the need to terminate affected ongoing pregnancies. New developments are directed towards improving both the timing and/or safety of procedures. Preimplantation genetic diagnosis, an established procedure with 20 years of clinical application, avoids the need to terminate affected pregnancies through the identification and selective transfer of unaffected in vitro fertilization embryos. Approaches towards 'noninvasive' PND, through analyzing fetal cells or free fetal DNA present in the circulation of pregnant women, are a focus of ongoing research. Overall, PND, preimplantation genetic diagnosis (and potentially 'noninvasive' PND) represent valuable reproductive options for couples at risk of having a child affected with a severe inherited disease.
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Affiliation(s)
- Joanne Traeger-Synodinos
- Department of Medical Genetics, National and Kapodistrian University of Athens, St Sophia's Children's Hospital, Athens 11527, Greece.
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Sirichotiyakul S, Wanapirak C, Saetung R, Sanguansermsri T. High resolution DNA melting analysis: an application for prenatal control of alpha-thalassemia. Prenat Diagn 2010; 30:348-51. [PMID: 20225225 DOI: 10.1002/pd.2480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To report the use of real-time gap-PCR using SYTO9 with high-resolution melting analysis (HRMA) in prenatal diagnosis of alpha-thalassemia 1. MATERIALS AND METHODS Real-time gap-PCR using SYTO9 with HRMA was performed in 33 DNA samples from chorionic villi sampling (8 normal, 16 heterozygous, and 9 homozygous) to determine the alpha-thalassemia 1 gene [normal and Southeast Asia (-SEA) allele]. RESULT The dissociation curve analysis in normal and - SEA allele gave a peak of T(m) at 91.80 +/- 0.14 degrees C and 88.67 +/- 0.08 degrees C, respectively. Normal genotype and homozygous alpha-thalassemia 1 showed a single peak of T(m) that corresponded to their alleles. The heterozygotes gave both peaks with higher normal peak and smaller - SEA peak. Thirty one samples showed consistent results with the conventional gap-PCR. Two samples with ambiguous results were confirmed to be maternal DNA contamination on real-time quantitative PCR and microsatellite assay. HRMA from both samples showed similar pattern to that of heterozygotes. However, they showed much smaller normal peak compared with the - SEA peak, which is in contrast to those of heterozygotes and can readily be distinguished. CONCLUSION HRMA with SYTO9 is feasible for prenatal diagnosis of alpha-thalassemia. It had potential advantage of prompt detection maternal DNA contamination.
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Affiliation(s)
- Supatra Sirichotiyakul
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
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Lien KY, Liu CJ, Kuo PL, Lee GB. Microfluidic System for Detection of α-Thalassemia-1 Deletion Using Saliva Samples. Anal Chem 2009; 81:4502-9. [DOI: 10.1021/ac900453d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kang-Yi Lien
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Chien-Ju Liu
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Pao-Lin Kuo
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
| | - Gwo-Bin Lee
- Institute of Nanotechnology and Microsystems Engineering, Department of Engineering Science, Department of Obstetrics and Gynecology, Medical College, National Cheng Kung University, Tainan 701, Taiwan, and Medical Electronics and Device Technology Center, Industrial Technology Research Institute, Hsinchu 310, Taiwan
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Pornprasert S, Kaewbundit A, Phusua A, Suanta S, Saetung R, Sanguansermsri T. Comparison of real-time polymerase chain reaction SYBR Green1 with high resolution melting analysis and TaqMan MGB probes for detection of alpha-thalassemia-1 South-East Asian type on dried blood spots. Eur J Haematol 2008; 81:405-407. [PMID: 18691321 DOI: 10.1111/j.1600-0609.2008.01137.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Sakorn Pornprasert
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang-Mai University, Chiang-Mai, Thailand
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Pornprasert S, Sukunthamala K, Sacome J, Phusua A, Saetung R, Sanguansermsri T, Leechanachai P. Analysis of real-time SYBR-polymerase chain reaction cycle threshold for diagnosis of the alpha-thalassemia-1 Southeast Asian type deletion: application to carrier screening and prenatal diagnosis of Hb Bart's hydrops fetalis. Hemoglobin 2008; 32:393-402. [PMID: 18654890 DOI: 10.1080/03630260701798367] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Without gel electrophoresis and specific probes, the two tubes real-time SYBR-polymerase chain reaction (SYBR-PCR) was setup by using different primer sets: P1/P2 for the detection of wild type alpha-globin gene alleles and P1/P3 for detection of the allele bearing the Southeast Asian (SEA) type (--SEA) deletion. Analyses of the cycle threshold (CT) values obtained by each primer set together with a delta-cycle threshold (DeltaCT) and CT ratio, showed that lower CT values generated by primer sets P1/P2 and P1/P3 were observed in normal and Hb Bart's hydrops fetalis subjects, respectively. In heterozygous subjects the CT values generated by both sets of primers were similar to each other. There was no overlapping of DeltaCT and CT ratio between normal, heterozygous and Hb Bart's hydrops fetalis subjects. Therefore, the two tubes real-time SYBR-PCR could represent a rapid, cost effective, high-throughput assay for screening of carriers and prenatal diagnosis of alpha-thalassemia-1 (alpha-thal-1) with the SEA type (--SEA) deletion.
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Affiliation(s)
- Sakorn Pornprasert
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang-Mai University, Chiang-Mai, Thailand
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Pornprasert S, Phusua A, Suanta S, Saetung R, Sanguansermsri T. Detection of alpha-thalassemia-1 Southeast Asian type using real-time gap-PCR with SYBR Green1 and high resolution melting analysis. Eur J Haematol 2008; 80:510-4. [PMID: 18284625 DOI: 10.1111/j.1600-0609.2008.01055.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alpha-thalassemia-1 Southeast Asian (SEA) type is the most common genetic disorder in the Asian population. Couples who are both carriers have a 25% chance of conceiving Bart's hydrops fetalis. Therefore, results from carrier screening and prenatal diagnosis frequently need to be available rapidly. A rapid technique for diagnosis of alpha-thalassemia-1 SEA type was implemented. The technique used is based on real-time gap-PCR and high resolution melting (HRM) analysis of the amplified fragment using the Rotor-Gene 6000. The DNA samples used for amplification were obtained from whole blood, cord blood, and chorionic villus sampling (CVS). With this method, the alpha-thalassemia-1 SEA allele can be easily distinguished from wild type alpha-globin gene allele. The real-time gap-PCR and HRM analysis offers additional benefits including minimal labor, rapid turnaround time, and a decreased risk of PCR carryover contamination. It is cost-effective and safe, does not require fluorescently labeled probe and hazardous chemicals. Moreover, it is accurate showing 100% concordance with conventional gap-PCR analysis.
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Affiliation(s)
- Sakorn Pornprasert
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang-Mai University, Chiang-Mai, Thailand.
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Traeger-Synodinos J. Real-time PCR for prenatal and preimplantation genetic diagnosis of monogenic diseases. Mol Aspects Med 2006; 27:176-91. [PMID: 16430951 DOI: 10.1016/j.mam.2005.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The provision of prenatal diagnosis requires the highest standards in laboratory practice to ensure an accurate result. In preimplantation genetic diagnosis protocols additionally have to address the need to achieve an accurate result from 1 to 2 cells within a limited time. Emerging protocols of "non-invasive" prenatal diagnosis, which are based on analysis of free fetal DNA in the circulation of the pregnant mother, also have to achieve a result from a limited quantity of fetal DNA against a high background of maternal free DNA. Real-time PCR uses fluorescent probes or dyes and dedicated instruments to monitor the accumulation of amplicons produced throughout the progress of a PCR reaction. Real-time PCR can be used for quantitative or qualitative evaluation of PCR products and is ideally suited for analysis of nucleotide sequence variations (point mutations) and gene dosage changes (locus deletions or insertions/duplications) that cause human monogenic diseases. Real-time PCR offers a means for more rapid and potentially higher throughput assays, without compromising accuracy and has several advantages over end-point PCR analysis, including the elimination of post-PCR processing steps and a wide dynamic range of detection with a high degree of sensitivity. This review will focus on real-time PCR protocols that are suitable for genotyping monogenic diseases with particular emphasis on applications to prenatal diagnosis, non-invasive prenatal diagnosis and preimplantation genetic diagnosis.
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Affiliation(s)
- Joanne Traeger-Synodinos
- Department of Medical Genetics, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, Athens 11527, Greece.
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Timmann C, Moenkemeyer F, Evans JA, Foerster B, Tannich E, Haase S, Sievertsen J, Kohne E, Horstmann RD. Diagnosis of alpha+-thalassemias by determining the ratio of the two alpha-globin gene copies by oligonucleotide hybridization and melting curve analysis. Clin Chem 2005; 51:1711-3. [PMID: 16120949 DOI: 10.1373/clinchem.2005.051375] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christian Timmann
- Department of Molecular Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, and Institute of Medical Biometry and Statistics, University Hospital Schleswig-Holstein-Campus Lübeck, Lübeck, Germany.
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Patrinos GP, Kollia P, Papadakis MN. Molecular diagnosis of inherited disorders: lessons from hemoglobinopathies. Hum Mutat 2005; 26:399-412. [PMID: 16138310 DOI: 10.1002/humu.20225] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hemoglobinopathies constitute a major health problem worldwide, with a high carrier frequency, particularly in certain regions where malaria has been endemic. These disorders are characterized by a vast clinical and hematological phenotypic heterogeneity. Over 1,200 different genetic alterations that affect the DNA sequence of the human alpha-like (HBZ, HBA2, HBA1, and HBQ1) and beta-like (HBE1, HBG2, HBG1, HBD, and HBB) globin genes are mainly responsible for the observed clinical heterogeneity. These mutations, together with detailed information about the resulting phenotype, are documented in the globin locus-specific HbVar database. Family studies and comprehensive hematological analyses provide useful insights for accurately diagnosing thalassemia at the DNA level. For this purpose, numerous techniques can provide accurate, rapid, and cost-effective identification of the underlying genetic defect in affected individuals. The aim of this article is to review the diverse methodological and technical platforms available for the molecular diagnosis of inherited disorders, using thalassemia and hemoglobinopathies as a model. This article also attempts to shed light on issues closely related to thalassemia diagnostics, such as prenatal and preimplantation genetic diagnoses and genetic counseling, for better-quality disease management.
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Affiliation(s)
- George P Patrinos
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, MGC-Department of Cell Biology and Genetics, Rotterdam, The Netherlands.
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dos Santos CO, Duarte ASS, Saad STO, Costa FF. Expression of alpha-hemoglobin stabilizing protein gene during human erythropoiesis. Exp Hematol 2004; 32:157-62. [PMID: 15102476 DOI: 10.1016/j.exphem.2003.11.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Revised: 10/14/2003] [Accepted: 11/05/2003] [Indexed: 11/29/2022]
Abstract
alpha-Hemoglobin stabilizing protein (AHSP) is an abundant, erythroid-specific protein that forms a stable complex with free alpha-hemoglobin but not with beta-hemoglobin or hemoglobin A. As such, AHSP is required for normal erythropoiesis, probably acting by blocking the deleterious effects of free alpha-hemoglobin precipitation. In order to study the levels of expression of the AHSP gene during the different phases of erythropoiesis, we carried out a two-phase liquid culture of erythroid cells and real-time quantitative polymerase chain reaction. Blood from control volunteers was cultured with erythropoietin to stimulate differentiation. The different stages of erythropoiesis were confirmed by morphologic and flow cytometric analysis. The results showed a progressive increase in AHSP gene expression following the expression of alpha-globin gene, during maturation of the red blood cell precursors, confirming the probable important function of this protein during normal erythropoiesis.
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