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Hussain M, Khan HN, Abbas S, Ali A, Aslam MN, Awan FR. Tetra-ARMS-PCR assay development for genotyping of AGT rs699 T/C polymorphism, its comparison with PCR-RFLP and application in a case-control association study of cardiovascular disease patients. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023:1-16. [PMID: 36815563 DOI: 10.1080/15257770.2023.2181972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Genetic variations in the AGT gene play a significant role in controlling the plasma concentration of angiotensinogen (precursor protein of bioactive octapeptide angiotensin II) and the efficacy of antihypertensive drugs. In the current study, Tetra-Amplification Refractory Mutation System-Polymerase Chain Reaction (T-ARMS-PCR) was developed for genotyping of AGT rs699 T/C polymorphism and validated through Sanger DNA sequencing. Its efficiency was also tested using 474 human DNA samples [control, n = 181; cardiovascular disease (CVD) patients, n = 293]. Results showed that T-ARMS-PCR is superior to the commonly used PCR-Restriction Fragment Length Polymorphism (PCR-RFLP). Statistical analysis revealed that the AGT rs699 CC genotype is more prevalent in the CVD patient group (37% vs. 28%) and AGT rs699 C allele and CC genotype increased the risk of CVD by 1.4 and 1.9 fold, respectively. In summary, T-ARMS-PCR is the most suitable approach for quick and efficient genotyping of AGT rs699 T/C polymorphism in a large population in resource-limited countries, Furthermore, AGT rs699 T/C polymorphism is associated with the risk of CVD in the Punjabi Pakistani population.
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Affiliation(s)
- Misbah Hussain
- Diabetes and Cardio-Metabolic Disorders Lab, Human Molecular Genetics and Metabolic Disorders Group, Health Biotechnology, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Department of Biotechnology, University of Sargodha, Sargodha, Pakistan.,NIBGE College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Islamabad, Pakistan
| | - Haq Nawaz Khan
- Diabetes and Cardio-Metabolic Disorders Lab, Human Molecular Genetics and Metabolic Disorders Group, Health Biotechnology, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,NIBGE College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Islamabad, Pakistan.,Department of Biological & Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Shahid Abbas
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Ansar Ali
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | | | - Fazli Rabbi Awan
- Diabetes and Cardio-Metabolic Disorders Lab, Human Molecular Genetics and Metabolic Disorders Group, Health Biotechnology, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,NIBGE College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Islamabad, Pakistan
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Tan Y, Jian H, Zhang R, Wang J, Zhou C, Xiao Y, Liang W, Wang L. Applying amplification refractory mutation system technique to detecting cell-free fetal DNA for single-gene disorders purpose. Front Genet 2023; 14:1071406. [PMID: 37113995 PMCID: PMC10128035 DOI: 10.3389/fgene.2023.1071406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Non-invasive prenatal diagnosis for single-gene disorders (NIPD) is still in development and deserves further study. The advent of next-generation sequencing technology significantly improved the detection of multiple mutations for non-invasive prenatal diagnosis for single-gene disorder purposes. However, bespoke amplicon-based NGS assays are costly. In this study, we developed a new strategy for non-invasive prenatal screening for single-gene disorders based on a capillary electrophoresis (CE) platform using an amplification refractory mutation system (ARMS)-PCR technique. Allele-specific primers for several disease-correlated mutations were designed, and subsequently, sensitivity and specificity assays were conducted. Assays on simulated two-person DNA mixtures showed that three primers targeting the mutant allele could detect minor DNA components in 1:500 mixtures. All primers showed positive results at 0.01 ng of the template DNA. Cell-free fetal DNA was extracted from a pregnant woman's peripheral blood for the detection of paternally inherited mutations. Our results showed that one primer successfully amplified the mutant allele of fetal DNA in maternal plasma, which was confirmed by genotyping the genomic DNA extracted from amniotic fluid. This study suggested that the ARMS-PCR technique, a fast and cost-effective method, might be a promising method used to target de novo or paternally inherited pathogenic mutations in maternal plasma.
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Affiliation(s)
- Yu Tan
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Hui Jian
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Cong Zhou
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Yuanyuan Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Weibo Liang, ; Li Wang,
| | - Li Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
- *Correspondence: Weibo Liang, ; Li Wang,
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Huebner T, Steffens M, Scholl C. Molecular Genetic Techniques in Biomarker Analysis Relevant for Drugs Centrally Approved in Europe. Mol Diagn Ther 2021; 26:89-103. [PMID: 34905151 PMCID: PMC8766366 DOI: 10.1007/s40291-021-00567-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 11/26/2022]
Abstract
On the basis of scientific evidence, information on the option, recommendation or requirement to test for pharmacogenetic or pharmacogenomic biomarkers is incorporated in the Summary of Product Characteristics of an increasing number of drugs in Europe. A screening of the Genetic Testing Registry (GTR) showed that a variety of molecular genetic testing methods is currently offered worldwide in testing services with regard to according drugs and biomarkers. Thereby, among the methodology indicated in the screened GTR category ‘Molecular Genetics’, next-generation sequencing is applied for identification of the largest proportion of evaluated biomarkers that are relevant for therapeutic management of centrally approved drugs in Europe. However, sufficient information on regulatory clearances, clinical utility, analytical and clinical validity of applied methods is rarely provided.
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Affiliation(s)
- Tatjana Huebner
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany.
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
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Designing PCR Primers for the Amplification-Refractory Mutation System. Methods Mol Biol 2021. [PMID: 34773617 DOI: 10.1007/978-1-0716-1799-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The recent development in genetic research indicates that there exists intraspecific genetic variability in many organism groups. These variations, which result in a variety of genotypes and phenotypes within a population, are called polymorphism. Mutations in different ways can alter the organism's phenotype and affect its fitness, for example, by altering disease susceptibility or resistance. Therefore, the detection of point mutations in different genes of a population is of particular importance. The amplification-refractory mutation system technique is a PCR-based method to detect single nucleotide polymorphisms in the genome. The high repeatability, low cost, high accessibility, and no need for sophisticated technology are the main advantages of the ARMS-PCR technique, compared with other available methods such as PCR-RFLP. This chapter describes the design and analysis method of primers for the ARMS-PCR technique.
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Imani S, Cheng J, Fu J, Mobasher-Jannat A, Wei C, Mohazzab-Torabi S, Jadidi K, Khosravi MH, Shasaltaneh MD, Yang L, Khan MA, Fu J. Novel splicing variant c. 208+2T>C in BBS5 segregates with Bardet-Biedl syndrome in an Iranian family by targeted exome sequencing. Biosci Rep 2019; 39:BSR20181544. [PMID: 30850397 PMCID: PMC6438871 DOI: 10.1042/bsr20181544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 01/13/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a rare genetically heterogeneous ciliopathy which accompanies retinitis pigmentosa (RP). However, the BBS5 mutation remains unclear in Iranians with BBS. The purpose of study is to evaluate genetic analyses of a BBS Iranian family using targetted exome sequencing (TES). A male 11-year-old proband and three related family members were recruited. Biochemical tests, electrocardiography and visual acuity testing, such as funduscopic, fundus photography (FP), optical coherence tomography (OCT), and standard electroretinography, were conducted. Molecular analysis and high-throughput DNA sequence analysis were performed. The proband was diagnosed with possible BBS based on the presence of three primary features and two secondary features. The TES analysis of the proband with BBS resulted in the identification of a novel, homozygous splicing variant c. 208+2T>C of the BBS5 gene (NM_152384.2) in this Iranian BBS family. This variant was confirmed and was completely co-segregated with the disease in this family by Sanger sequencing. Thus, we report a novel, homozygous splicing site variant c.208+2T>C in the BBS5 gene for the first time in the Iranian family.
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Affiliation(s)
- Saber Imani
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
- Institute of Medical Technology, Xiangtan Medicine and Health Vocational College, Xiangtan, Hunan, China
| | | | - Chunli Wei
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | | | - Khosrow Jadidi
- Department of Ophthalmology, Bina Eye Hospital Research Center, Tehran, Iran
| | | | | | - Lisha Yang
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Md Asaduzzaman Khan
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
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Huang J, Fu J, Fu S, Yang L, Nie K, Duan C, Cheng J, Li Y, Lv H, Chen R, Liu L, Fu J. Diagnostic value of a combination of next-generation sequencing, chorioretinal imaging and metabolic analysis: lessons from a consanguineous Chinese family with gyrate atrophy of the choroid and retina stemming from a novel OAT variant. Br J Ophthalmol 2018; 103:428-435. [PMID: 30366948 DOI: 10.1136/bjophthalmol-2018-312347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 10/11/2018] [Accepted: 10/13/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND/AIM Gyrate atrophy of the choroid and retina (GACR) is an extremely rare autosomal recessive inherited disorder characterised by progressive vision loss. To identify the disease-causing gene in a consanguineous Chinese pedigree with GACR, we aimed to accurately diagnose patients with GACR through a combination of next-generation sequencing (NGS) genetic diagnosis, clinical imaging and amino acid metabolic analysis. METHODS A consanguineous Chinese pedigree with GACR, including two patients, was recruited and a comprehensive ophthalmological evaluation was performed. DNA was extracted from a proband and her family members, and the sample from the proband was analysed using targeted NGS. Variants detected by NGS were confirmed by Sanger sequencing and subjected to segregation analysis. Tandem mass spectrometry (MS/MS) was subsequently performed for metabolic assessment. RESULTS We identified a novel, deleterious, homologous ornithine aminotransferase (OAT) variant, c.G248A: p.S83N, which contributes to the progression of GACR in patients. Our results showed that the p.S83N autosomal recessive variant of OAT is most likely pathogenic, with changes in protein stability drastically decreasing functionality. MS/MS verified that ornithine levels in patients were significantly elevated. CONCLUSIONS Recruitment of a third-degree first cousin consanguineous marriage family with GACR allowed us to identify a novel pathogenic OAT variant in the Chinese population, broadening the mutation spectrum. Our findings reported the diagnostic value of a combination of NGS, retinal imaging and metabolic analysis of consanguineous marriage pedigrees in low-income/middle-income and low-incidence countries, including China, and may help to guide accurate diagnosis and treatment of this disease.
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Affiliation(s)
- Junting Huang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Shangyi Fu
- The Honors College, University of Houston, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lisha Yang
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Kailai Nie
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Chengxia Duan
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Hongbin Lv
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Longqian Liu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
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