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Surati U, Niranjan SK. Development of PCR-based genetic test for detection of TTF1 mutation causing abortion in Holstein Friesian cattle. Reprod Domest Anim 2024; 59:e14581. [PMID: 38698693 DOI: 10.1111/rda.14581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/18/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024]
Abstract
A stop-gain mutation (rs715966442; BTA11: 1,02,463,944 nucleotide position) in transcription termination factor, RNA polymerase I (TTF1) gene causes abortion in Holstein Friesian (HF) cattle. A PCR-restriction fragment length polymorphism (PCR-RFLP)-based genetic test has been developed and validated to screen the TTF1 mutation locus in HF cattle. The mutation locus was screened in 80 HF and HF crossbreds using the protocol, which revealed two animals as carriers of the mutant TTF1 allele. The test employed is cost-effective, rapid and precise and can be utilized as an effective tool for the screening of TTF1 mutation carriers in HF cattle population.
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Affiliation(s)
- Utsav Surati
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
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2
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Khalil A, Khan HN, Wasim M, Ayesha H, Awan FR. Development of low-cost in-house tetra-ARMS-PCR assay for the screening of five CBS mutations found in Pakistani homocystinuria patients. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:517-529. [PMID: 37971987 DOI: 10.1080/15257770.2023.2280013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Classical homocystinuria is an inborn amino acid metabolism disorder resulting from mutations in the Cystathionine-β-Synthase (CBS) gene. These mutations lead to elevated homocysteine and methionine levels and reduced cysteine levels in the blood. Typically, diagnosis occurs after patients display symptoms, and various lab methods confirm it. DNA sequencing is the best option for early detection of genetic variants in asymptomatic suspected individuals. Unfortunately, its high cost can hinder its use, especially in low-income countries like Pakistan. OBJECTIVE Aim of this study was to devise a robust low-cost diagnostic/screening assay based on Tetra-ARMS-PCR for five prevalent genetic variants found in Pakistani classical homocystinuria patients. MATERIALS AND METHODS In the current study, T-ARMS-PCR assays were developed for five mutations (c.975G > C, c.770C > T, c.752T > C, c.1039 + 1G > T, c.451 + 1GG > TA), which were characterized previously in classical homocystinuria patients. These low-cost T-ARMS-PCR assays were then used to screen the affected individuals and their family members to identify their genotypes for pathogenic variations in the asymptomatic patients and carriers in their respective families. RESULTS The outcomes were entirely consistent with those obtained from Sanger DNA sequencing, confirming the sensitivity, specificity, and reliability of the T-ARMS-PCR assay for detecting CBS mutations. CONCLUSION T-ARMS-PCR has wide applications for low-income countries for the screening and early diagnosis of asymptomatic patients and carriers in the homocystinuria affected families as well as other inherited diseases.
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Affiliation(s)
- Adila Khalil
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- NIBGE College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Haq Nawaz Khan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- NIBGE College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Muhammad Wasim
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- NIBGE College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Hina Ayesha
- Department of Pediatrics, Punjab Medical College, Faisalabad Medical University, Faisalabad, Pakistan
| | - Fazli Rabbi Awan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- NIBGE College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
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Najd-Hassan-Bonab L, Hedayati M, Shahzadeh Fazeli SA, Daneshpour MS. An optimized method for PCR-based genotyping to detect human APOE polymorphisms. Heliyon 2023; 9:e21102. [PMID: 37954297 PMCID: PMC10637921 DOI: 10.1016/j.heliyon.2023.e21102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/10/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
Background Apolipoprotein E (APOE) is one of the most polymorphic genes at two single nucleotides (rs429358 and rs7412). The various isoforms of APOE have been associated with a variety of diseases, including neurodegenerative, type 2 diabetes, etc. Hence, predicting the APOE genotyping is critical for disease risk evaluation. The purpose of this study was to optimize the tetra amplification refractory mutation system (Tetra-ARMS) PCR method for the detection of APOE mutations. Material and methods Here, in our optimized Tetra-ARMS PCR method, different factors like cycle conditions, using HiFidelity enzyme instead of Taq polymerase and setting its best concentration, and the lack of using dimethylsulfoxide (DMSO) for amplifying the GC-regions were set up for all primer pairs. The sensitivity and accuracy were tested. For validation of the assay, the results were compared with known genotypes for the APOE gene that were previously obtained by two independent methods, RFLP and Chip-typing. Results Successful Tetra-ARMS PCR and genotyping are influenced by multiple factors. Our developed method enabled us to amplify the DNA fragment by 25 cycles without adding any hazardous reagent, like DMSO. Our findings showed 100 % accuracy and sensitivity of the optimized Tetra-ARMS PCR while both criteria were 95 % for RFLP and 100 % for the chip-typing method. In addition, our results showed 91 % and 100 % consistency with RFLP and chip typing methods, respectively. Conclusions Our current method is a simple and accurate approach for detecting APOE polymorphisms within a large sample size in a short time and can be performed even in low-tech laboratories.
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Affiliation(s)
- Leila Najd-Hassan-Bonab
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Abolhassan Shahzadeh Fazeli
- Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Maryam S. Daneshpour
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Shi P, Shen XJ, Chen JC, Zhang YJ, Cao LJ, Pang BS, Liu LH, Zhang MM, Hoffmann AA, Wei SJ. KASP genotyping and semi-quantitation of G275E mutation in the α6 subunit of Thrips palmi nAChR gene conferring spinetoram resistance. PEST MANAGEMENT SCIENCE 2023; 79:1777-1782. [PMID: 36627758 DOI: 10.1002/ps.7353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Pesticide resistance is a long-standing and growing problem in the chemical control of invertebrate pests. Molecular diagnostic methods can facilitate pesticide resistance management by accurately and efficiently detecting resistant mutations and their frequency. In this study, the kompetitive allele specific PCR (KASP) approach, a technology for high-throughput single nucleotide polymorphism (SNP) genotyping, is validated as a useful method for characterizing genotypes at a pesticide-resistance locus for the first time. We focus on the spinetoram resistance mutation of G275E in the nicotinic acetylcholine receptor alpha 6 (nAChR α6) subunit gene of Thrips palmi. RESULTS Of the 341 individuals of Thrips palmi tested, 98.24% were successfully genotyped, with 100% concordance with Sanger sequencing results. We then quantitatively mixed genomic DNA of known genotypes to establish 21 DNA mixtures with a resistant allele frequency ranging from 0 to 100% at steps of 5%. The linear discriminant analysis (LDA) showed that 75.8% of original grouped cases were correctly classified; six groups had no overlap in membership (resistant allele frequency: 0%, 5%, 10-75%, 80-85%, 90-95%, and 100%). When we chose 11 pooled samples with 10% steps for LDA, 84.4% of original grouped cases were correctly classified; seven groups had no overlap in membership (0%, 10%, 20-30%, 40-70%, 80%, 90%, 100%). The results indicated that KASP applied to pooled samples may provide a semi-quantitative estimate of resistance. CONCLUSIONS Our study points to the suitability of KASP for high-throughput genotyping of genotypes affecting pesticide resistance and semi-quantitative assessments of resistance allele frequencies in populations. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Pan Shi
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yu-Jie Zhang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Bin-Shuang Pang
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Hua Liu
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ming-Ming Zhang
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Australia
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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The association between single polymorphic positions and the risk of acute lymphoblastic leukemia. Meta Gene 2022. [DOI: 10.1016/j.mgene.2021.101006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kumar A, Gupta ID, Mohan G, M R V, D RK, S J, Kataria RS, Niranjan SK. Alternate PCR assays for screening of JH1 mutation associated with embryonic death in Jersey cattle. Mol Cell Probes 2020; 55:101688. [PMID: 33279530 DOI: 10.1016/j.mcp.2020.101688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
Jersey haplotype (JH) 1, a stop-gain lethal mutation in the CWC15 gene, causes embryonic losses in Jersey cattle. Two PCR based assays using Amplification Refractory Mutation System (T-ARMS-PCR) and restriction fragment length polymorphism (PCR-RFLP) were developed for screening of the JH1 in cattle. During the screening, seven among 30 Indian Jersey bulls were identified as carriers of the mutant JH1 allele, the first time in the country. These PCR assays are economical, rapid and accurate; and can be used separately or in combination for screening and cross-validation of the JH1 carriers in Jersey cattle.
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Affiliation(s)
- Anshuman Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Govind Mohan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vineeth M R
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Ravi Kumar D
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Jayakumar S
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Ranjit Singh Kataria
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India.
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Involvement of single nucleotide polymorphisms in acute lymphoblastic leukemia susceptibility. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Sabiha B, Haider SA, Jan H, Yousafzai YM, Afridi OK, Khan AA, Ali J. Development of the Next Generation Sequencing-Based Diagnostic Test for β-Thalassemia and its Validation in a Pashtun Family. Hemoglobin 2020; 44:254-258. [PMID: 32691635 DOI: 10.1080/03630269.2020.1793773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
β-Thalassemia (β-thal) is a common monogenic disease with ethnic-specific mutations on the HBB gene throughout the world. The reported mutations either reduce the expression or completely inactivate the HBB gene. In Pakistan, the prevalence of β-thal is high due to consanguineous marriages. Accurate identification of mutations in carriers is imperative for prevention of β-thal in subsequent generations. To overcome the limitations of traditional testing methods for β-thal, a next-generation sequencing (NGS)-based diagnostic test was designed and validated by sequencing the entire HBB gene. The primer set covering the entire HBB gene was designed and validated in a Pashtun β-thalassemic family. The polymerase chain reaction (PCR) product was sequenced using an Illumina MiSeq platform. A homozygous pathogenic insertion of A>AC/AC (rs35699606) was detected in an affected member of the family, while unaffected members were heterozygous for it. In addition, all family members were homozygous for the synonymous variant, A>G/G (rs713040), except the father who was heterozygous for it. We sequenced the entire HBB gene using the NGS-based test, which is highly sensitive, robust and specific for the diagnosis and screening of β-thal in Pakistan, especially for families practicing consanguineous marriages.
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Affiliation(s)
- Bibi Sabiha
- Center for Genome Sciences, Rehman Medical College (RMC), Peshawar, Khyber Pakhtunkhwa (KP), Pakistan
| | - Syed Adnan Haider
- Center for Genome Sciences, Rehman Medical College (RMC), Peshawar, Khyber Pakhtunkhwa (KP), Pakistan
| | - Hanifullah Jan
- Center for Genome Sciences, Rehman Medical College (RMC), Peshawar, Khyber Pakhtunkhwa (KP), Pakistan
| | - Yasar Mehmood Yousafzai
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, KP, Pakistan
| | - Ome Kalsoom Afridi
- CECOS-Rehman Medical Institute (RMI), Precision Medicine Laboratory, Peshawar, KP, Pakistan
| | - Abid Ali Khan
- Center of Biotechnology and Microbiology (COBAM), University of Peshawar, Peshawar, KP, Pakistan
| | - Johar Ali
- Center for Genome Sciences, Rehman Medical College (RMC), Peshawar, Khyber Pakhtunkhwa (KP), Pakistan.,Executive Development Center, Sukkur Institute of Business Administration (IBA) University, Sukkur, Sindh, Pakistan
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Kumar A, Gupta I, Mohan G, Vineeth M, Ravi kumar D, Jayakumar S, Niranjan S. Development of PCR based assays for detection of lethal Holstein haplotype 1, 3 and 4 in Holstein Friesian cattle. Mol Cell Probes 2020; 50:101503. [DOI: 10.1016/j.mcp.2019.101503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/18/2019] [Accepted: 12/26/2019] [Indexed: 11/26/2022]
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Mokhtarian R, Tabatabaeian H, Saadatmand P, Azadeh M, Balmeh N, Yakhchali B, Ghaedi K. CD44 Gene rs8193 C Allele Is Significantly Enriched in Gastric Cancer Patients. CELL JOURNAL 2020; 21:451-458. [PMID: 31376327 PMCID: PMC6722445 DOI: 10.22074/cellj.2020.6389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Gastric cancer is a multifactorial disease. In addition to environmental factors, many genes are involved in this malignancy. One of the genes associated with gastric cancer is CD44 gene and its polymorphisms. CD44 gene plays role in regulating cell survival, growth and mobility. The single nucleotide polymorphism (SNP) rs8193, located in the CD44 gene, has not been studied in gastric cancer patients of the Iranian population. The present study aims to study this polymorphism in 86 gastric cancer patients and 96 healthy individuals. MATERIALS AND METHODS In this cross-sectional case-control study, rs8193 polymorphism was genotyped by allele specific primer polymerase chain reaction (ASP-PCR) technique. The obtained data were statistically analyzed. To find the potential mechanism of action, rs8193 was bioinformatically investigated. RESULTS rs8193 C allele played a risk factor role for gastric cancer. Patients carrying this allele were more susceptible to have gastric cancer, with lymph node spread. On the other hand, rs8193 T allele, a protective factor, was associated with a higher chance of accumulation in the lower stages of cancer. C allele might impose its effect via destabilizing CD44 and miR-570 interaction. CONCLUSION rs8193 is statistically associated with the risk of malignancy, lymph node spread and stage of gastric cancer in Iranian population.
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Affiliation(s)
- Roya Mokhtarian
- Division of Cellular and Molecular Biology, Department of Biology, NourDanesh Institute of Higher Education, Meymeh, Iran
| | - Hossein Tabatabaeian
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | | | | | - Negar Balmeh
- Division of Cellular and Molecular Biology, Department of Biology, NourDanesh Institute of Higher Education, Meymeh, Iran
| | - Bagher Yakhchali
- Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology Institute, Tehran, Iran
| | - Kamran Ghaedi
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. Electronic Address:
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Gill P, Amree AH. Allele-Specific Loop-Mediated Isothermal Amplification for the Detection of IVSII-I G>A Mutation On β-Globin Gene. Open Access Maced J Med Sci 2019; 7:1582-1587. [PMID: 31210804 PMCID: PMC6560289 DOI: 10.3889/oamjms.2019.285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Thalassemia is one of the most common genetic health problems in the world. More than 200 different mutations have been identified in the beta-globin gene and among the 24 β-globin gene mutations in β-thalassemia carriers in the north of Iran IVSII-I G>A mutation has the highest frequency. Using fast, inexpensive, simple and reliable methods for the detection of the mutations in β-thal carriers is very important in prenatal diagnosis, and introduction of alternative methods to the existing ones can help to simplify the detection of mutations. Since its introduction, different methods derived from LAMP have been widely used for SNPs detection. AIM This study was aimed to design a new method for the detection of IVSII-I G>A mutation on β-globin gene based on AS - LAMP technique. METHODS Primer explorer V5 software was used for the design of LAMP primers. Three sets of primers were designed. In the first set, the BIP primers were exactly complementary to the normal and mutant alleles. In the second set, 1 nucleotide (T) was inserted at the 5' end of BIP primers, and in the last set, one nucleotide at the 5' end of BIP primer was changed. The other required primers for the LAMP reaction (FIP, B3, and F3) were the same for all 3 sets of primers. The LAMP reaction was applied on three DNA samples (Wild type, Heterozygote and Homozygote for IVSII-I G>A mutation) and synthetic DNA. RESULTS The results of the present study showed that LAMP reaction using three sets of primers could not successfully detect the IVSII-I G > A mutation among subjects DNA sample and synthetic DNA. CONCLUSION Although several studies have successfully used ARMS-LAMP method to detect the SNPs, and other studies use a variety of methods to identify IVSII-I G>A mutation, the present study was unable to differentiate between a normal allele and IVSII-I G>A mutation. Hence further studies are recommended to consider redesigning of primer set, DNA concentration and using commercial LAMP Master Mix to detect the mutation.
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Affiliation(s)
- Pooria Gill
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Sari, Iran.,Nano Medicine Group, Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Arash Hadian Amree
- Hemoglobinopathy Institute, Thalassemia Research Center, Mazandaran University of Medical Science, Sari, Iran
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Chao J, Chai L, Yin X, Zhou Z, Xu S, Zhu W, Deng Y. Application of Single-Tube Tri-Primer ARMS-PCR to Detect the NFKB1 ATTG Insertion/Deletion Polymorphism. Genet Test Mol Biomarkers 2018; 22:443-447. [PMID: 30020835 DOI: 10.1089/gtmb.2018.0034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS The -94 ATTG insertion/deletion polymorphism (rs28362491) is an important functional polymorphism in the NFKB1 gene. It has been shown that rs28362491 is associated with many diseases. The purpose of this study was to establish a simple and reliable method to detect the ATTG insertion/deletion polymorphism. METHODS On the basis of the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) method, a single-tube tri-primer ARMS-PCR method was developed to detect the ATTG insertion/deletion polymorphism in 93 samples. The results of the single-tube tri-primer ARMS-PCR method were validated by DNA sequencing. RESULTS After optimization of the PCR conditions, the single-tube tri-primer ARMS-PCR was established to detect the insertion/deletion polymorphism using agarose gel electrophoresis. In 93 volunteers, the genotype frequencies were 30.1% for Ins/Ins, 19.4% for Del/Del, and 50.5% for Ins/Del, respectively. The results of the single-tube tri-primer ARMS-PCR method were consistent with the results of DNA sequencing. CONCLUSIONS This single-tube tri-primer ARMS-PCR is a reliable, simple, and cost-efficient genotyping method for the detection of the ATTG insertion/deletion polymorphism in the NFKB1 gene.
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Affiliation(s)
- Jiashuo Chao
- 1 The First Clinic Medical College, School of Medicine, Nanchang University , Nanchang, Jiangxi, China
| | - Lina Chai
- 1 The First Clinic Medical College, School of Medicine, Nanchang University , Nanchang, Jiangxi, China
| | - Xiaolong Yin
- 2 Department of Ophthalmology of Children, The Second Affiliated Hospital, Nanchang University , Nanchang, Jiangxi, China
| | - Zhongqin Zhou
- 3 The Second Clinic Medical College, School of Medicine, Nanchang University , Nanchang, Jiangxi, China
| | - Suming Xu
- 3 The Second Clinic Medical College, School of Medicine, Nanchang University , Nanchang, Jiangxi, China
| | - Weifeng Zhu
- 4 Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Nanchang University , Nanchang, Jiangxi, China
| | - Yan Deng
- 2 Department of Ophthalmology of Children, The Second Affiliated Hospital, Nanchang University , Nanchang, Jiangxi, China
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Mansouri Bidkani M, Tabatabaeian H, Parsafar S, Ghanei N, Fazilati M, Ghaedi K. ErbB4 receptor polymorphism 2368A>C and risk of breast cancer. Breast 2018; 42:157-163. [PMID: 30336339 DOI: 10.1016/j.breast.2018.10.002] [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: 06/18/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022] Open
Abstract
PURPOSE A number of single nucleotide polymorphisms (SNPs) in EebB4 gene have been studied, which has clarified their impact on breast cancer in different populations. Nevertheless, the importance of rs13423759 in breast cancer has not been studied and its effect remained almost unclear. In this paper, we evaluated the frequency of rs13423759 different alleles in Iranian population and statistically analyzed their association with breast cancer risk. MATERIALS AND METHODS Allele-specific Primer PCR (ASP-PCR) was recruited in this study to genotype rs13423759 position in 172 breast cancer and 148 healthy control subjects. The genotypes of control and cases were analyzed statistically to find the association between rs13423759 alleles and breast cancer incidence and its clinicopathological characteristics. In silico studies were performed in order to find the mechanistic viewpoint of rs13423759 alleles in breast cancer. RESULTS rs13423759 allele C was shown to be significantly associated with breast cancer risk, HER2 positivity and increased risk of metastasis. Reciprocally, allele A was correlated with the lowered risk of breast cancer. The in silico studies showed that rs13423759 allele C is capable to strengthen the interaction between miR-548as, an oncomiRNA, and ErbB4 mRNA, leading to its lowered concentration in the cells. CONCLUSION rs13423759 allele C is significantly associated with the enhanced risk of breast cancer, elevated metastasis and HER2 positivity.
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Affiliation(s)
| | - Hossein Tabatabaeian
- Division of Genetics, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Soha Parsafar
- Division of Genetics, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Nafezeh Ghanei
- Department of Biochemistry, Payam e Noor University, Isfahan, Iran
| | | | - Kamran Ghaedi
- Division of Cellular and Molecular Biology, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran; Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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TP53 rs1625895 is Related to Breast Cancer Incidence and Early Death in Iranian Population. Indian J Clin Biochem 2018; 34:485-489. [PMID: 31686737 DOI: 10.1007/s12291-018-0774-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/16/2018] [Indexed: 12/29/2022]
Abstract
Breast cancer as the second most common cancer worldwide tend to be experienced by Iranian women 10 years earlier with a peak incidence at the premenopausal stage. Genetic mutations of TP53 tumor suppressor gene has been shown to be related to early onset of breast cancer. It has been shown already that rs1625895 polymorphic site is related to glioma as well as lung cancer. In this study, we have investigated the role of rs1625895 polymorphism in breast cancer incidence in Iranian women. DNA extraction of 86 breast cancer patients and 96 control individuals have been used for allele-specific primer-PCR and genotyping of allele A and allele G of the TP53 rs1625895. Genotypes frequencies have been shown that GG homozygosis as the most frequent genotype is a significant association with increased risk of breast cancer development in Iranian women (odds ratio = 6, p = 0.002). On the other hand and in comparison to allele G, allele A could cause early death of breast cancer patients by threefolds significantly (p = 0.011). As a conclusion, we show that allele A is the minor allele in both breast cancer patients and also control individuals and major allele G, is related to the increased risk of breast cancer development in Iranian women.
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15
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Jin Y, Yang Q, Zhang M, Zhang S, Cai H, Dang R, Lei C, Chen H, Lan X. Identification of a Novel Polymorphism in Bovine lncRNA ADNCR Gene and Its Association with Growth Traits. Anim Biotechnol 2018; 30:159-165. [DOI: 10.1080/10495398.2018.1456446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yunyun Jin
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Qing Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Meng Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Hanfang Cai
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Ruihua Dang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
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16
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ESR1 single nucleotide polymorphism rs1062577 (c.*3804T > A) alters the susceptibility of breast cancer risk in Iranian population. Gene 2017; 611:9-14. [DOI: 10.1016/j.gene.2017.02.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 11/20/2022]
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17
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Zhang S, Dang Y, Zhang Q, Qin Q, Lei C, Chen H, Lan X. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) rapidly identified a critical missense mutation (P236T) of bovine ACADVL gene affecting growth traits. Gene 2015; 559:184-8. [PMID: 25620159 DOI: 10.1016/j.gene.2015.01.043] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
Abstract
Acyl-CoA dehydrogenase, very long chain (ACADVL), encoding ACADVL protein, targets the inner mitochondrial membrane where it catalyzes the first step of the mitochondrial fatty acid beta-oxidation pathway and plays an important role in body metabolism and oxidation of long chain fatty acid releasing energy. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is an easy-to-operate, rapid, inexpensive, and exact method for SNP genotyping. Herein, T-ARMS-PCR was carried out to detect a critical missense mutation (AC_000176:g.2885C>A; Pro236Thr) within the ACADVL gene in 644 individuals from two cattle breeds. In order to evaluate the accuracy of the T-ARMS-PCR at this locus, the genotype of the sampled individuals was also identified by PCR-RFLP. The concordance between these two methods was 98.76%. Statistical analysis showed that the bovine ACADVL gene had a significant effect on chest width (P<0.05), chest depth (P<0.05), and hip width (P<0.05) in the Qinchuan breed. The cattle with AA genotype had superior growth traits compared to cattle with AC and/or CC genotypes. The "A" allele had positive effects on growth traits. Therefore, T-ARMS-PCR can replace PCR-RFLP for rapid genotyping of this mutation, which could be used as a DNA marker for selecting individuals with superior growth traits in the Qinchuan breed. These findings contribute to breeding and genetics in beef cattle industry.
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Affiliation(s)
- Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
| | - Yonglong Dang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Qingfeng Zhang
- College of Life Sciences, Heze University, Heze, Shangdong 274015, China
| | - Qiaomei Qin
- College of Life Sciences, Heze University, Heze, Shangdong 274015, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
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