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Pan TY, Kou HS, Wu SM, Wang CC. Identifiable universal fluorescent multiplex PCR equipped with capillary electrophoresis for genotyping of exons 1 to 5 in human red and green pigment genes. Talanta 2022; 241:123199. [PMID: 35033897 DOI: 10.1016/j.talanta.2021.123199] [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: 10/05/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/27/2022]
Abstract
Congenital red and green color blindness is the most X-linked recessive disorder in humans caused by deletions or gross structural rearrangements of the visual pigment gene array that lead to altered the functions of visual pigments in their retina differ from normal. The incidence is about 7-10% in male and close association of X-linked recessive disorders (such as: hemophilia A, hemophilia B, duchenne muscular dystrophy). However, the traditional genetic analysis methods are time-consuming and low-efficiencies. Therefore, the purpose of the study is to develop a rapid method for genotyping of red and green pigment genes. We describe herein the first method for simultaneous evaluation of ten exons in the red and green pigment genes for genetic analysis. A forward specific primers with identifiable universal fluorescent multiplex PCR (FSIUFM-PCR) method utilized one universal primer (containing two universal non-human sequences) and forward specific primers in the multiplex PCR reaction system for simultaneously fluorescent labeling of eleven gene fragments (ten exons in red and green pigment genes and one internal standard). All the PCR products were analyzed on capillary electrophoresis with short-end injection, which had the advantage of high resolution and rapid separation. Of all 80 detected individuals, 7 subjects with color vision deficiencies (including 3 subjects only had red exons 1-5, 4 subjects had a specific red-green or green-red hybrid gene and 73 subjects with normal color vision). All genotyping results showed good agreement with DNA sequencing data. This method provided a better potential technique for genotyping and identifying of red and green pigment genes. In addition, FSIUFM-PCR method will be useful in many fields, such as diagnosis of diseases, analysis of polymorphisms and quantitative assay.
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Affiliation(s)
- Tzu-Yu Pan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Hwang-Shang Kou
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Shou-Mei Wu
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC.
| | - Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC; Drug Development and Value Creation Research Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC.
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Ou SF, Ho CS, Lee WT, Lin KL, Jones CC, Jong YJ. Natural history in spinal muscular atrophy Type I in Taiwanese population: A longitudinal study. Brain Dev 2021; 43:127-134. [PMID: 32878721 DOI: 10.1016/j.braindev.2020.07.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/30/2020] [Accepted: 07/16/2020] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Spinal muscular atrophy (SMA) is caused by a defect in the survival motor neuron 1 (SMN1) gene. The Cooperative Study of the natural history of SMA Type I in Taiwan is a retrospective, longitudinal, observational study that helps in further understanding SMA disease progression in patients who have not received disease-modifying therapeutic interventions. METHODS Case report forms were used to collect demographics; genetic confirmation; SMN2 copy number; treatment patterns; and clinical outcomes including ventilator use, endotracheal tube intubation, tracheostomy, gastrostomy, complications, and survival. RESULTS A total of 111 patients with SMA Type I were identified over the study period (1979-2015). Mean (median) age of onset and age at confirmed diagnosis were 1.3 (0.8) and 4.9 (4.4) months, respectively. SMN1 deletion/mutation was documented in 70 patients and SMN2 copy number in 32 (2 copies, n = 20; 3 copies, n = 12). At 240 months, survival probability for patients born during 1995-2015 versus 1979-1994 was significantly longer (p = 0.0057). Patients with 3 SMN2 copies showed substantially longer 240-month survival versus patients with 2 SMN2 copies. Over the 36-year period, mean (median) age at death was 31.9 (8.8) months. As of December 2015, 95 patients had died, 13 were alive, and 3 were lost to follow-up. The use of supportive measures (tracheostomy and gastrostomy) was associated with improved survival. CONCLUSIONS These data describe the short survival of patients with SMA Type I in Taiwan in the pretreatment era, emphasizing the positive impact of supportive measures on survival.
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Affiliation(s)
- Shan-Fu Ou
- Department of Pediatrics, Antai Medical Care Cooperation Antai Tian-Sheng Memorial Hospital, Pingtung, Taiwan
| | - Che-Sheng Ho
- Division of Pediatric Neurology, Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan; Department of Medicine, MacKay Medical College, New Taipei, Taiwan
| | - Wang-Tso Lee
- Department of Pediatrics, National Taiwan University Hospital, and National Taiwan University, College of Medicine, Taipei, Taiwan
| | - Kuang-Lin Lin
- Division of Pediatric Neurology, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Cynthia C Jones
- Department of Epidemiology, Global Analytics and Data Sciences, Biogen, Cambridge, MA, USA
| | - Yuh-Jyh Jong
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Departments of Pediatrics and Laboratory Medicine, and Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
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Molecular inversion probe-rolling circle amplification with single-strand poly-T luminescent copper nanoclusters for fluorescent detection of single-nucleotide variant of SMN gene in diagnosis of spinal muscular atrophy. Anal Chim Acta 2020; 1123:56-63. [PMID: 32507240 DOI: 10.1016/j.aca.2020.04.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/31/2020] [Accepted: 04/10/2020] [Indexed: 11/21/2022]
Abstract
In this study, a simple fluorescent detection of survival motor neuron gene (SMN) in diagnosis of spinal muscular atrophy (SMA) based on nucleic acid amplification test and the poly-T luminescent copper nanoclusters (CuNCs) was established. SMA is a severely genetic diseases to cause infant death in clinical, and detection of SMN gene is a powerful tool for pre- and postnatal diagnosis of this disease. This study utilized the molecular inversion probe for recognition of nucleotide variant between SMN1 (c.840 C) and SMN2 (c.840 C > T) genes, and rolling circle amplification with a universal primer for production of poly-T single-strand DNA. Finally, the fluorescent CuNCs were formed on the poly-T single-strand DNA template with addition of CuSO4 and sodium ascorbate. The fluorescence of CuNCs was only detected in the samples with the presence of SMN1 gene controlling the disease of SMA. After optimization of experimental conditions, this highly efficient method was performed under 50 °C for DNA ligation temperature by using 2U Ampligase, 3 h for rolling circle amplification, and the formation of the CuNCs by mixing 500 μM Cu2+ and 4 mM sodium ascorbate. Additionally, this highly efficient method was successfully applied for 65 clinical DNA samples, including 4 SMA patients, 4 carriers and 57 wild individuals. This label-free detection strategy has the own potential to not only be a general method for detection of SMN1 gene in diagnosis of SMA disease, but also served as a tool for detection of other single nucleotide polymorphisms or nucleotide variants in genetic analysis through designing the different sensing probes.
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Wang CC, Chen CA, Jong YJ, Kou HS. Specific Gene Capture Combined with Restriction-Fragment Release for Directly Fluorescent Genotyping of Single-Nucleotide Polymorphisms in Diagnosing Spinal Muscular Atrophy. Anal Chem 2018; 90:11599-11606. [PMID: 30203652 DOI: 10.1021/acs.analchem.8b02996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, a fast and simple fluorescent genotyping strategy, streptavidin magnetic beads combined with biotin-coupled PCR and restriction-fragment release, was developed for determination of nucleotide variants. This method was further applied for analyzing SMN1 gene in diagnosis of spinal muscular atrophy (SMA). After biotin-coupled PCR, the streptavidin magnetic beads would capture the biotin-labeled SMN genetic fragments, and then the restriction enzyme of HPY188I could only digest and release the fluorescent end of SMN1 genetic fragment into the supernatant. Therefore, the SMN1 gene could be easily fluorescently quantified, and SMN2 would not, for diagnosis of SMA. The copy number of the SMN1 gene could be regressed using the relative fluorescent unit versus the known copy number, and the coefficient of correlation is equal to 0.9617 ( r = 0.9617). In this research, a total of 16 blind DNA samples were analyzed, including 6 wild types, 5 carriers, and 5 SMA patients. Importantly, this fast, simple, and highly efficient method is universal for detection of all nucleotides variants by replacing the specific restriction enzyme. This technique has the potency to be served as a tool for fast and accurate diagnosis of genotypes in clinical medicine.
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Affiliation(s)
| | - Chung-An Chen
- Institute of Applied Mechanics , National Taiwan University , Taipei , Taiwan
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Kou HS, Wang CC. Molecular inversion probes equipped with discontinuous rolling cycle amplification for targeting nucleotide variants: Determining SMN1 and SMN2 genes in diagnosis of spinal muscular atrophy. Anal Chim Acta 2017; 977:65-73. [PMID: 28577599 DOI: 10.1016/j.aca.2017.04.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
Abstract
The novel techniques of molecular inversion probes (MIPs) combined with discontinuous rolling cycle amplification (DRCA) was developed for determination of the multi-nucleotide variants at single base. The different-length MIPs, a padlock-probe based technology, are designed to simultaneously recognize the identical nucleotide variants. After ligation and DRCA, the different-length genetic products representing the certain genotypes could be simply determined by the short-end capillary electrophoresis (CE) method. By using MIPs-DRCA method, the various gene dosages of SMN1 and SMN2 genes in homologous or heterologous subjects were successfully quantified for diagnosis of spinal muscular atrophy (SMA). The length of the MIP for SMN1 gene was 106 bp, and for SMN2 gene was 86 bp. After method optimization, the MIP products of SMN1 and SMN2 were well separated with the resolution of 1.13 ± 0.17 (n = 3) within 10 min. There were total of 56 DNA blind samples analyzed by this strategy, including 38 wild types, 12 carriers and 6 SMA patients, and the data of gene dosages was corresponding to those analyzed by conformation sensitive CE and denatured high performance liquid chromatography (DHPLC) methods. This MIPs-DRCA method which could be applied to simultaneously genotype multi nucleotide variants at single base, such as K-ras gene, was very feasible for determination of genetic diseases in clinical.
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Affiliation(s)
- Hwang-Shang Kou
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Li L, Zhou WJ, Fang P, Zhong ZY, Xie JS, Yan TZ, Zeng J, Tan XH, Xu XM. Evaluation and comparison of three assays for molecular detection of spinal muscular atrophy. Clin Chem Lab Med 2017; 55:358-367. [PMID: 27754957 DOI: 10.1515/cclm-2016-0275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/29/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is mainly caused by deletions in SMA-related genes. The objective of this study was to develop gene-dosage assays for diagnosing SMA. METHODS A multiplex, quantitative PCR assay and a CNVplex assay were developed for determining the copy number of SMN1, SMN2, and NAIP. Reproducibility and specificity of the two assays were compared to a multiple ligation-dependent probe amplification (MLPA) assay. To evaluate reproducibility, 30 samples were analyzed three times using the three assays. A total of 317 samples were used to assess the specificity of the two assays. RESULTS The multiplex quantitative PCR (qPCR) assay had higher reproducibility. Intra-assay CVs were 3.01%-8.52% and inter-assay CVs were 4.12%-6.24%. The CNVplex assay had ratios that were closer to expected (0.49-0.5 for one copy, 1.03-1.0 for two copies, and 1.50-1.50 for three copies). Diagnostic accuracy rates for the two assays were 100%. CONCLUSIONS The multiplex qPCR assay was a simple, rapid, and cost-effective method for routine SMA diagnosis and carrier screening. The CNVplex assay could be used to detect SMAs with complicated gene structures. The assays were reliable and could be used as alternative methods for clinical diagnosis of SMA.
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Lin TL, Chen TH, Hsu YY, Cheng YH, Juang BT, Jong YJ. Selective Neuromuscular Denervation in Taiwanese Severe SMA Mouse Can Be Reversed by Morpholino Antisense Oligonucleotides. PLoS One 2016; 11:e0154723. [PMID: 27124114 PMCID: PMC4849667 DOI: 10.1371/journal.pone.0154723] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/18/2016] [Indexed: 11/27/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive motor neuron disease caused by deficiency of the survival of motor neuron (SMN) protein, which leads to synaptic defects and spinal motor neuron death. Neuromuscular junction (NMJ) abnormalities have been found to be involved in SMA pathogenesis in the SMNΔ7 SMA mouse model. However, whether similar NMJ pathological findings present in another commonly used mouse model, the Taiwanese SMA mouse, has not been fully investigated. To examine the NMJs of the Taiwanese severe SMA mouse model (Smn-/-; SMN2tg/0), which is characterized by severe phenotype and death before postnatal day (P) 9, we investigated 25 axial and appendicular muscles from P1 to P9. We labelled the muscles with anti-neurofilament and anti-synaptophysin antibodies for nerve terminals and α-bungarotoxin for acetylcholine receptors (AChRs). We found that severe NMJ denervation (<50% fully innervated endplates) selectively occurred in the flexor digitorum brevis 2 and 3 (FDB-2/3) muscles from P5, and an increased percentage of fully denervated endplates correlated with SMA progression. Furthermore, synaptophysin signals were absent at the endplate compared to control littermate mice, suggesting that vesicle transport might only be affected at the end stage. Subsequently, we treated the Taiwanese severe SMA mice with morpholino (MO) antisense oligonucleotides (80 μg/g) via subcutaneous injection at P0. We found that MO significantly reversed the NMJ denervation in FDB-2/3 muscles and extended the survival of Taiwanese severe SMA mice. We conclude that early NMJ denervation in the FDB-2/3 muscles of Taiwanese severe SMA mice can be reversed by MO treatment. The FDB-2/3 muscles of Taiwanese severe SMA mice provide a very sensitive platform for assessing the effectiveness of drug treatments in SMA preclinical studies.
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Affiliation(s)
- Te-Lin Lin
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tai-Heng Chen
- Division of Pediatric Emergency, Department of Emergency, Kaohsiung Medical University and Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ya-Yun Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Hua Cheng
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Bi-Tzen Juang
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yuh-Jyh Jong
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Molecular Medicine and Bioengineering, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Departments of Pediatrics and Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail: ;
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Ahmadpour‐Yazdi H, Hormozi‐Nezhad MR, Abadi AR, Sanati MH, Kazemi B. Colourimetric‐based method for the diagnosis of spinal muscular atrophy using gold nanoprobes. IET Nanobiotechnol 2015; 9:5-10. [DOI: 10.1049/iet-nbt.2013.0065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Hossein Ahmadpour‐Yazdi
- Department of Medical Physics and Biomedical EngineeringSchool of MedicineShahid Beheshti University of Medical SciencesTehran 1985717443Iran
| | - Mohammad Reza Hormozi‐Nezhad
- Department of ChemistrySharif University of TechnologyTehran 11155‐9516Iran
- Institute for Nanoscience and NanotechnologySharif University of TechnologyTehran 14588‐89694Iran
| | - Ali Reza Abadi
- Department of Health and Community MedicineSchool of MedicineShahid Beheshti University of Medical SciencesTehran 1985717443Iran
| | - Mohammad Hossein Sanati
- Department of Medical BiotechnologyNational Institute of Genetic Engineering and Biotechnology (NIGEB)Shahrak‐e‐Pajoohesh, 15th km, Tehran‐Karaj HighwayTehran 14965‐161Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research CenterShahid Beheshti University of Medical SciencesTehran 19395‐4719Iran
- Department of BiotechnologySchool of MedicineShahid Beheshti University of Medical SciencesTehran 19395‐4719Iran
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Pan TY, Chiou SS, Wang CC, Wu SM. Separation of intron 22 inversion type 1 and 2 of hemophilia A by modified inverse-shifting polymerase chain reaction and capillary gel electrophoresis. Talanta 2014; 130:328-35. [DOI: 10.1016/j.talanta.2014.06.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/28/2014] [Accepted: 06/30/2014] [Indexed: 10/25/2022]
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Genotyping of intron 22 inversion of factor VIII gene for diagnosis of hemophilia A by inverse-shifting polymerase chain reaction and capillary electrophoresis. Anal Bioanal Chem 2014; 406:5447-54. [DOI: 10.1007/s00216-014-7969-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/02/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
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Universal fluorescent tri-probe ligation equipped with capillary electrophoresis for targeting SMN1 and SMN2 genes in diagnosis of spinal muscular atrophy. Anal Chim Acta 2014; 833:40-7. [PMID: 24909772 DOI: 10.1016/j.aca.2014.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 01/02/2023]
Abstract
This is the first ligase chain reaction used for diagnosis of spinal muscular atrophy (SMA). Universal fluorescent tri-probe ligation (UFTPL), a novel strategy used for distinguishing the multi-nucleotide alternations at single base, is developed to quantitatively analyze the SMN1/SMN2 genes in diagnosis of SMA. Ligase chain reaction was performed by adding three probes including universal fluorescent probe, connecting probe and recognizing probe to differentiate single nucleotide polymorphisms in UFTPL. Our approach was based on the two UFTPL products of survival motor neuron 1 (SMN1) and SMN2 genes (the difference of 9 mer) and analyzed by capillary electrophoresis (CE). We successfully determined various gene dosages of SMN1 and SMN2 genes in homologous or heterologous subjects. By using the UFTPL-CE method, the SMN1 and SMN2 genes were fully resolved with the resolution of 2.16±0.37 (n=3). The r values of SMN1 and SMN2 regression curves over a range of 1-4 copies were above 0.9944. Of the 48 DNA samples, the data of gene dosages were corresponding to that analyzed by conformation sensitive CE and denatured high-performance liquid chromatography (DHPLC). This technique was found to be a good methodology for quantification or determination of the relative genes having multi-nucleotide variants at single base.
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Chen CA, Wang CC, Chen YL, Jong YJ, Wu SM. A “turn on/off” scorpion biosensor targeting point mutation of SMN genes for diagnosis of spinal muscular atrophy. Chem Commun (Camb) 2014; 50:8069-72. [DOI: 10.1039/c4cc03472d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Capillary electrophoretic genotyping of epidermal growth factor receptor for pharmacogenomic assay of lung cancer therapy. J Chromatogr A 2012; 1256:276-9. [PMID: 22901298 DOI: 10.1016/j.chroma.2012.07.087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 07/19/2012] [Accepted: 07/26/2012] [Indexed: 11/21/2022]
Abstract
In this research, a universal multiplex PCR method combining capillary gel electrophoresis was established for simultaneous analysis of mutations in exons 18-21 of EGFR kinase domain gene. After rinsing of the gel solution (1 × TBE buffer containing 2% HEC and 1.5% HPC), the diluted PCR sample was electrokinetically injected and separated at 35°C. Several parameters were investigated for method optimization, including the kinds of polymer, capillary temperature and separation voltage. Under optimal conditions, time taken for analyzing mutations of EGFR kinase domain gene in lung cancer patients was short (within 15 min). A total of 50 lung cancer patients' tumor tissues were analyzed, and two frequent mutations associated with therapeutic efficiency of lung cancer were identified, including deletion of exon 19 (8/50) and L858R point mutation in exon 21 (12/50). This method is feasible for application in pharmacogenomic assay of lung cancer therapy. By applying this simple and effective method for genotyping of lung cancer patients, the information of pharmacogenomics was supplied for lung cancer therapy and to assist diagnosis to prolong patients' lives.
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Liao YM, Lin SK, Liu TC, Chiou SS, Lu HC, Kao CF, Chang JG. Rapid identification of the copy number of α-globin genes by capillary electrophoresis analysis. Clin Biochem 2012; 45:798-805. [PMID: 22374170 DOI: 10.1016/j.clinbiochem.2012.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 01/19/2012] [Accepted: 02/09/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVES The current study aimed at the rapid identification of the copy number of α-globin genes for the diagnosis of α-thalassemia. DESIGN AND METHODS To identify the copy number of α-globin genes in α-thalassemia, we developed a novel method using a multiplex polymerase chain reaction (PCR) in combination with the CE analysis. RESULTS The proposed method provides a rapid detection of the common α-globin gene deletions. Sixty-six patients with α-thalassemia and 46 normal controls were included in the present study. The obtained results showed good correlation with those obtained by gap PCR. Moreover, a low amount of maternal cell contamination in the fetus specimen for the prenatal diagnosis of hemoglobin Barts hydrops fetalis as well as the rare multiplicated α-globin genes can be identified using this method. CONCLUSION This method provides a convenient and efficient tool for the rapid identification of the copy number of α-globin genes in α-thalassemia and the individuals with α-globin gene multiplication.
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Affiliation(s)
- Yu-Mei Liao
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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Chen TH, Tzeng CC, Wang CC, Wu SM, Chang JG, Yang SN, Hung CH, Jong YJ. Identification of bidirectional gene conversion between SMN1 and SMN2 by simultaneous analysis of SMN dosage and hybrid genes in a Chinese population. J Neurol Sci 2011; 308:83-7. [PMID: 21705024 DOI: 10.1016/j.jns.2011.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by programmed motoneuron death. The survival motor neuron 1 (SMN1) gene is an SMA-determining gene and SMN2 represents an SMA-modifying gene. Here, we applied capillary electrophoresis to quantify the SMN gene dosage in 163 normal individuals, 94 SMA patients and 138 of their parents. We further quantified exons 7 and 8 in SMN1 and SMN2. We found that the SMA patients carried the highest SMN2 copies, which was inversely correlated with disease severity among its three subtypes. Increased SMN1 was significantly associated with decreased SMN2 in the normal group. We also observed that parents of type I SMA patients had significantly fewer SMN2 copies than those of types II and III patients. The hybrid SMN genes were detected in two normal individuals and one patient and her mother. These results imply that increased SMN2 copies in SMA patient group might be derived from SMN1-to-SMN2 conversion, whereas the trend that normal individuals with higher SMN1 copies simultaneously carry fewer SMN2 copies suggested a reverse conversion, SMN2-to-SMN1. Together with the identification of hybrid SMN genes, our data provided additional evidence to support that SMN1 and SMN2 gene loci are interchangeable between population groups.
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Affiliation(s)
- Tai-Heng Chen
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
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Cheng HL, Chiou SS, Liao YM, Chen YL, Wu SM. Genotyping of single nucleotide polymorphism in γ-glutamyl hydrolase gene by capillary electrophoresis. Electrophoresis 2011; 32:2021-7. [DOI: 10.1002/elps.201000422] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/03/2010] [Accepted: 11/16/2010] [Indexed: 12/14/2022]
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Wang CC, Chang JG, Chen YL, Jong YJ, Wu SM. Multi-exon genotyping of SMN gene in spinal muscular atrophy by universal fluorescent PCR and capillary electrophoresis. Electrophoresis 2010; 31:2396-404. [PMID: 20564270 DOI: 10.1002/elps.201000124] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this study, we established the first method for simultaneous evaluation of nine exons in the survival motor neuron (SMN) genes for full-scale genotyping. This method was used not only to quantify the copy numbers of highly homogenous telomeric SMN (SMN1)/centromeric SMN genes in exons 7 and 8 but also to determine intragenic mutations in all nine exons for complete diagnosis of spinal muscular atrophy (SMA). Additionally, we utilized the "universal fluorescent PCR" for simultaneously fluorescent labeling of eleven gene fragments (nine exons in SMN and two internal standards). Such technique is very beneficial for multi-exon analysis due to only requirement of one universal fluorescent primer which could fluorescently amplify all gene fragments. Of all 262 detected individuals, three subjects possessing different ratios of SMN1/centromeric SMN in the two exons were determined as gene conversion, and we also detected three interesting intragenic mutations (c.1 -39A>G, c.22_23insA in exon 1, c.84C>T in exon 2a) which were associated with the SMA patients owning one copy of SMN1 including two mutations never reported previously. This high-resolved method provided better potential technique for genotyping and identifying SMA, carrier and normal controls in large population.
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Affiliation(s)
- Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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Wang CC, Jong YJ, Chang JG, Chen YL, Wu SM. Universal fluorescent multiplex PCR and capillary electrophoresis for evaluation of gene conversion between SMN1 and SMN2 in spinal muscular atrophy. Anal Bioanal Chem 2010; 397:2375-83. [PMID: 20563565 DOI: 10.1007/s00216-010-3761-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 04/15/2010] [Accepted: 04/15/2010] [Indexed: 12/24/2022]
Abstract
We have developed a capillary electrophoresis (CE) method with universal fluorescent multiplex PCR to simultaneously detect the SMN1 and SMN2 genes in exons 7 and 8. Spinal muscular atrophy (SMA) is a very frequent inherited disease caused by the absence of the SMN1 gene in approximately 94% of patients. Those patients have deletion of the SMN1 gene or gene conversion between SMN1 and SMN2. However, most methods only focus on the analysis of whole gene deletion, and ignore gene conversion. Simultaneous quantification of SMN1 and SMN2 in exons 7 and 8 is a good strategy for estimating SMN1 deletion or SMN1 to SMN2 gene conversion. This study established a CE separation allowing differentiation of all copy ratios of SMN1 to SMN2 in exons 7 and 8. Among 212 detected individuals, there were 23 SMA patients, 45 carriers, and 144 normal subjects. Three individuals had different ratios of SMN1 to SMN2 in two exons, including an SMA patient having two SMN2 copies in exon 7 but one SMN1 copy in exon 8. This method could provide more information about SMN1 deletion or SMN1 to SMN2 gene conversion for SMA genotyping and diagnosis.
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Affiliation(s)
- Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan
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Sukenik-Halevy R, Pesso R, Garbian N, Magal N, Shohat M. Large-Scale Population Carrier Screening for Spinal Muscular Atrophy in Israel—Effect of Ethnicity on the False-Negative Rate. Genet Test Mol Biomarkers 2010; 14:319-24. [DOI: 10.1089/gtmb.2009.0089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rivka Sukenik-Halevy
- Rabin Medical Center, Recanati Institute of Medical Genetics, Petach Tikva, Israel
| | - Rachel Pesso
- Genetic Institute of Maccabi Health Insurance, Mega-Lab, Rehovot, Israel
| | - Noa Garbian
- Genetic Institute of Maccabi Health Insurance, Mega-Lab, Rehovot, Israel
| | - Nurit Magal
- Rabin Medical Center, Recanati Institute of Medical Genetics, Petach Tikva, Israel
| | - Mordechai Shohat
- Rabin Medical Center, Recanati Institute of Medical Genetics, Petach Tikva, Israel
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Affiliation(s)
- Nicholas W. Frost
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455
| | - Meng Jing
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455
| | - Michael T. Bowser
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455
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Baris I, Etlik O, Koksal V, Arican-Baris ST. Rapid diagnosis of spinal muscular atrophy using tetra-primer ARMS PCR assay: simultaneous detection of SMN1 and SMN2 deletion. Mol Cell Probes 2009; 24:138-41. [PMID: 20025960 DOI: 10.1016/j.mcp.2009.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 11/15/2009] [Accepted: 12/02/2009] [Indexed: 01/02/2023]
Abstract
Spinal muscular atrophy (SMA), the leading genetic cause of death in childhood, is an autosomal recessive neuromuscular disorder characterized by progressive muscle weakness, associated with deletions of the survival motor neuron 1 (SMN1) gene. Approximately 94% of SMA patients carry homologous deletions of SMN1 exon(s) 7 (and 8). Because of the high incidence and severity of the disease, precise detection and quantification of SMN1 and SMN2 gene copy numbers is essential for diagnosis and genetic counseling. We have developed a reliable single-tube tetra-primer PCR assay to simultaneously detect both the SMN1 and SMN2 exon 7 deletion using the advantage of C/T difference at nucleotide position of 840 in exon 7. The assay has been optimized and tested in 48 healthy controls, 20 known patients with SMA, 12 carriers (one SMN1 copy), and 8 amniotic fluids suspected of having SMA for whom we had determined the SMN1/SMN2 deletion by an additional PCR-RFLP method. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for simultaneous detection of both SMN1 and SMN2 deletion, which could be used even in "low-tech" laboratories.
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Affiliation(s)
- Ibrahim Baris
- Department of Chemical and Biological Engineering, KOC University, Istanbul, Turkey.
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Wang CC, Chang JG, Jong YJ, Wu SM. Universal multiplex PCR and CE for quantification ofSMN1/SMN2genes in spinal muscular atrophy. Electrophoresis 2009; 30:1102-10. [DOI: 10.1002/elps.200800375] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Huska D, Hubalek J, Adam V, Kizek R. Miniaturized electrochemical detector as a tool for detection of DNA amplified by PCR. Electrophoresis 2008; 29:4964-71. [DOI: 10.1002/elps.200800445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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