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Li S, Gu Y, Geng Z, Li K, Hu Y, Liu Q, Fu R, Liu P. Tweezer PCR: A Highly Specific Method for Accurate Identification of Low-Abundance Mutations. Anal Chem 2023; 95:17679-17690. [PMID: 37971891 DOI: 10.1021/acs.analchem.3c03467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Somatic mutation is a valuable biomarker for tracking tumor progression and migration due to its distinctive feature in various tumors and its wide distribution throughout body fluids. However, accurately detecting somatic mutations from the abundant DNA of noncancerous origins remains a practical challenge in the clinic. Herein, we developed an ultraspecific method, called tweezer PCR, for detecting low-abundance mutations inspired by the design of DNA origami. The high specificity of tweezer PCR relies on a tweezer-shaped primer containing six basic functional units: a primer, a hairpin, a linker, a blocker, a spacer, and a toehold. After optimizing the structure of the tweezer-shaped primer and enhancing its specificity by adding additional Mg2+ and Na+, tweezer PCR distinguished as low as 20 copies of mutations from 2 million copies of wild-type templates per test. By testing synthesized plasmids and plasma samples gathered from nonsmall-cell lung cancer patients, tweezer PCR showed higher specificity and robustness for detecting low-copy-number mutations in contrast with digital droplet PCR. Additionally, the need for conventional instruments makes tweezer PCR a practically accessible method for testing low-abundance mutations. Because of its numerous advantages, we believe that tweezer PCR offers a precise, robust, and pragmatic tool for cancer screening, prognosis, and genotyping in the clinic.
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Affiliation(s)
- Shanglin Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
| | - Yin Gu
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Zhi Geng
- Shimadzu Research Laboratory (Shanghai) Co. Ltd, Shanghai 201206, China
| | - Kaiyi Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yawei Hu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
| | - Qiang Liu
- Beijing Haidian Hospital, Beijing 100080, China
| | - Rongxin Fu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
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Saito Y, Tada F, Takashina T, Ikegami H. Allele-Specific Mutation Genotyping with Mismatches in Primer Design. Methods Mol Biol 2023; 2638:249-262. [PMID: 36781647 DOI: 10.1007/978-1-0716-3024-2_17] [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: 02/15/2023]
Abstract
Genotyping technologies for single nucleotide polymorphisms (SNPs) and other mutation types have evolved to become essential tools in various fields. Although high-throughput genotyping technologies occupy a key position in handling large amounts of SNP data, simple, low-cost, and conventional genotyping technologies remain in demand. Allele-specific (AS) polymerase chain reaction (PCR) and its related improved methods can effectively identify target SNPs and allele types using AS primers that introduce instability through mismatched bases at and around the SNP site. In this chapter, we present what is known from the literature on primer design with mismatches for AS-PCR and describe three cases of mutation detection (SNPs and insertions/deletions) associated with functional genes of crop species, which could be useful to guide future AS-PCR experiments.
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Affiliation(s)
- Yutaro Saito
- Yamagata Integrated Agricultural Research Center, Horticultural Research Institute, Yamagata, Japan
| | - Fumito Tada
- Yamagata Integrated Agricultural Research Center, Horticultural Research Institute, Yamagata, Japan
| | - Tadashi Takashina
- Yamagata Integrated Agricultural Research Center, Horticultural Research Institute, Yamagata, Japan
| | - Hidetoshi Ikegami
- Fukuoka Agriculture and Forestry Research Center, Buzen Branch, Yukuhashi, Japan.
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Molecular Determination of Vascular Endothelial Growth Factor, miRNA-423 Gene Abnormalities by Utilizing ARMS-PCR and Their Association with Fetal Hemoglobin Expression in the Patients with Sickle Cell Disease. Curr Issues Mol Biol 2022; 44:2569-2582. [PMID: 35735616 PMCID: PMC9221959 DOI: 10.3390/cimb44060175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
Recent studies have indicated that microRNA and VEGF are considered to be genetic modifiers and are associated with elevated levels of fetal haemoglobin HbF, and thus they reduce the clinical impact of sickle haemoglobin (HbS) patients. This cross-sectional study was performed on clinical confirmed subjects of SCD cases. miR-423-rs6505162 C>T and VEGF-2578 C>A genotyping was conducted by ARMS-PCR in SCD and healthy controls. A strong clinical significance was reported while comparing the association of miR-423 C>T genotypes between SCD patients and controls (p = 0.031). The microRNA-423 AA genotype was associated with an increased severity of SCD in codominant model with odd ratio (OR = 2.36, 95% CI, (1.15–4.84), p = 0.018) and similarly a significant association was observed in recessive inheritance model for microRNA-423 AA vs (CC+CA) genotypes (OR = 2.19, 95% CI, (1.32–3.62), p < 0.002). The A allele was associated with SCD severity (OR = 1.57, 95% CI, (1.13–2.19), p < 0.007). The distribution of VEGF-2578 C>A genotypes between SCD patients and healthy controls was significant (p < 0.013). Our results indicated that in the codominant model, the VEGF-2578-CA genotype was strongly associated with increased SCD severity with OR = 2.56, 95% CI, (1.36–4.82), p < 0.003. The higher expression of HbA1 (65.9%), HbA2 (4.40%), was reported in SCD patients carrying miR-423-AA genotype than miR-423 CA genotype in SCD patients carrying miR-423 CA genotype HbA1 (59.98%), HbA2 (3.74%) whereas SCD patients carrying miR-423 CA genotype has higher expression of HbF (0.98%) and HbS (38.1%) than in the patients carrying AA genotype HbF (0.60%), HbS (36.1%). ARMS-PCR has been proven to be rapid, inexpensive and is highly applicable to gene mutation screening in laboratories and clinical practices. This research highlights the significance of elucidating genetic determinants that play roles in the amelioration of the HbF levels that is used as an indicator of severity of clinical complications of the monogenic disease. Further well-designed studies with larger sample sizes are necessary to confirm our findings.
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Tortajada-Genaro LA. Design of Oligonucleotides for Allele-Specific Amplification Based on PCR and Isothermal Techniques. Methods Mol Biol 2022; 2392:35-51. [PMID: 34773613 DOI: 10.1007/978-1-0716-1799-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-nucleotide variations have been associated to various genetic diseases, variations on drug efficiency, and differences in cancer prognostics. The detection of these changes in nucleic acid sequences from patient samples is particularly useful for accurate diagnosis, therapeutics, and disease management. A reliable allele-specific amplification is still an important challenge for molecular-based diagnostic technologies. In the last years, allele-specific primers have been designed for promoting the enrichment of certain variants, based on a higher stability of primer/template duplexes. Also, several methods are based on the addition of a blocking oligonucleotide that prevent the amplification of a specific variant, enabling that other DNA variants can be observed. In this context, genotyping methods based on isothermal amplification techniques are increasing, especially those assays aimed to be deployed at point-of-care applications. The correct selection of target sequences is crucial for reaching the required analytical performances, in terms of reaction time, amplification yield, and selectivity. The present chapter describes the design criteria for the selection of primers and blockers for relevant PCR approaches and novel isothermal strategies. Several successful examples are provided in order to highlight the main design restrictions and the potential to be extended to other applications.
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Affiliation(s)
- Luis Antonio Tortajada-Genaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Valencia, Spain.
- Departamento de Química, Universitat Politècnica de València, Valencia, Spain.
- Unidad Mixta UPV-La Fe, Nanomedicine and sensors, Valencia, Spain.
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Li B, Liu Y, Hao X, Dong J, Chen L, Li H, Wu W, Liu Y, Wang J, Wang Y, Li P. Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping. BMC Genomics 2021; 22:850. [PMID: 34819030 PMCID: PMC8611915 DOI: 10.1186/s12864-021-08148-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The detection and identification of single nucleotide polymorphism (SNP) is essential for determining patient disease susceptibility and the delivery of medicines targeted to the individual. At present, SNP genotyping technology includes Sanger sequencing, TaqMan-probe quantitative polymerase chain reaction (qPCR), amplification-refractory mutation system (ARMS)-PCR, and Kompetitive Allele-Specific PCR (KASP). However, these technologies have some disadvantages: the high cost of development and detection, long and time consuming protocols, and high false positive rates. Focusing on these limitations, we proposed a new SNP detection method named universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR). In this method, only two types of fluorescence-labeled probes were used for SNP genotyping, thus greatly reducing the cost of development and detection for SNP genotyping. RESULTS In the amplification process of UPIP-qPCR, unlabeled intermediate primers with template-specific recognition functions could trigger probe hydrolysis and specific signal release. UPIP-qPCR can be used successfully and widely for SNP genotyping. The sensitivity of UPIP-qPCR in SNP genotyping was 0.01 ng, the call rate was more than 99.1%, and the accuracy was more than 99.9%. High-throughput DNA microarrays based on intermediate primers can be used for SNP genotyping. CONCLUSION This novel approach is both cost effective and highly accurate; it is a reliable SNP genotyping method that would serve the needs of the clinician in the provision of targeted medicine.
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Affiliation(s)
- Baowei Li
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Key Laboratory of Antibody Medicines, School of Bioscience and Technology, Weifang Medical University, Jinan, 261053, Shandong, China. .,Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China.
| | - Yanran Liu
- School of Basic Medicine, Qingdao University, Qingdao, 266021, China
| | - Xiaodan Hao
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Jinhua Dong
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Key Laboratory of Antibody Medicines, School of Bioscience and Technology, Weifang Medical University, Jinan, 261053, Shandong, China
| | - Limei Chen
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Key Laboratory of Antibody Medicines, School of Bioscience and Technology, Weifang Medical University, Jinan, 261053, Shandong, China
| | - Haimei Li
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Key Laboratory of Antibody Medicines, School of Bioscience and Technology, Weifang Medical University, Jinan, 261053, Shandong, China
| | - Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ying Liu
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Jianxun Wang
- School of Basic Medicine, Qingdao University, Qingdao, 266021, China
| | - Yin Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China.
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A novel and quick PCR-based method to genotype mice with a leptin receptor mutation (db/db mice). Acta Pharmacol Sin 2018; 39:117-123. [PMID: 28748911 DOI: 10.1038/aps.2017.52] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/05/2017] [Indexed: 12/16/2022] Open
Abstract
db/db mice is one of most widely used animal models in studying the cellular and molecular mechanisms of metabolic disorders, such as diabetes, hyperlipidemia, and obesity. The mice carry spontaneous point mutations in the gene encoding the leptin receptor, leading to leptin receptor inactivation. Since homozygous db/db mice are sterile, the maintenance of db/db mice requires breeding between heterozygous pairs, which makes genotyping essential for the identification of offspring. The aim of this study was to develop a quick and highly repeatable method for genotyping db/db mice, which comprised only three simple steps: genomic DNA is extracted from either tail tips or ear notches via alkaline lysis (∼20 min); samples are then subjected to tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) using specially designed and validated primer sets (∼1.5 h); finally, genotypes are be determined by resolving PCR products on regular DNA electrophoresis (∼10 min). The entire db/db mice genotyping procedure can be performed using regular Taq polymerase and PCR amplification within 2 h. Other advantages of this method include high sensitivity and reproducibility. Minimal amounts of tissue from mice are required, and genomic DNA samples can be stably stored at room temperature for up to one month. In conclusion, the method is simple, cost effective, sensitive and reliable, which will greatly facilitate studies using db/db mice.
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Yang L, Ijaz I, Cheng J, Wei C, Tan X, Khan MA, Fu X, Fu J. Evaluation of amplification refractory mutation system (ARMS) technique for quick and accurate prenatal gene diagnosis of CHM variant in choroideremia. APPLICATION OF CLINICAL GENETICS 2017; 11:1-8. [PMID: 29296092 PMCID: PMC5741072 DOI: 10.2147/tacg.s144383] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Choroideremia is a rare X-linked recessive inherited disorder that causes chorioretinal dystrophy leading to visual impairment in its early stages which finally causes total blindness in the affected person. It is caused due to mutations in the CHM gene. In this study, we have recruited a pedigree with choroideremia and detected a nonsense variant (c.C799T:p.R267X) in CHM of the proband (I:1). Different primer sets for amplification refractory mutation system (ARMS) were designed and PCR conditions were optimized. Then, we evaluated the sequence variant in the patient, carrier, and a fetus by using ARMS technique to identify if they inherited the pathogenic gene from parental generation; we used amniotic fluid DNA for the diagnosis of the gene in the fetus. The primer pairs, WT2+C and MT+C, amplified high specific products in different DNAs which were verified by Sanger sequencing. Based on our results, ARMS technique is fast, accurate, and reliable prenatal gene diagnostic tool to assess CHM variants. Taken together, our study indicates that ARMS technique can be used as a potential molecular tool in the diagnosis of prenatal mutation for choroideremia as well as other genetic diseases in undeveloped and developing countries, where there might be shortage of medical resources and supplies.
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Affiliation(s)
- Lisha Yang
- Key Laboratory of Epigenetics and Oncology, the Research Center for Precision Medicine, Southwest Medical University, Luzhou
| | - Iqra Ijaz
- Key Laboratory of Epigenetics and Oncology, the Research Center for Precision Medicine, Southwest Medical University, Luzhou
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, the Research Center for Precision Medicine, Southwest Medical University, Luzhou.,Department of Pathology, Hunan Normal University College of Medicine, Changsha
| | - Chunli Wei
- Key Laboratory of Epigenetics and Oncology, the Research Center for Precision Medicine, Southwest Medical University, Luzhou.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR)
| | - Xiaojun Tan
- Reproductive and Genetic Center, the Central Hospital of Xiangtan City, Xiangtan
| | - Md Asaduzzaman Khan
- Key Laboratory of Epigenetics and Oncology, the Research Center for Precision Medicine, Southwest Medical University, Luzhou
| | - Xiaodong Fu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Precision Medicine, Southwest Medical University, Luzhou.,Department of Pathology, Hunan Normal University College of Medicine, Changsha.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR)
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Franke M, Baeßler B, Vechtel J, Dafinger C, Höhne M, Borgal L, Göbel H, Koerber F, Maintz D, Benzing T, Schermer B, Persigehl T. Magnetic resonance T2 mapping and diffusion-weighted imaging for early detection of cystogenesis and response to therapy in a mouse model of polycystic kidney disease. Kidney Int 2017; 92:1544-1554. [DOI: 10.1016/j.kint.2017.05.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/03/2017] [Accepted: 05/25/2017] [Indexed: 12/19/2022]
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Iurlo A, Gianelli U, Beghini A, Spinelli O, Orofino N, Lazzaroni F, Cambiaghi S, Intermesoli T, Rambaldi A, Cortelezzi A. Identification of kit(M541L) somatic mutation in chronic eosinophilic leukemia, not otherwise specified and its implication in low-dose imatinib response. Oncotarget 2015; 5:4665-70. [PMID: 25015329 PMCID: PMC4148089 DOI: 10.18632/oncotarget.1941] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Activating mutations of KIT receptor tyrosine kinase have been reported in different neoplasms. The M541L KIT substitution (KITM541L) has been described to be associated with pediatric mastocytosis, to enhance growth rate of the affected cells and to confer higher sensitivity to imatinib therapy. We investigated the presence of KITM541L in five males with chronic eosinophilic leukemia, not otherwise specified (CEL, NOS), all negative for Platelet-derived growth factor-alpha (PDGFR) or PDGFRbeta abnormalities, which responded to imatinib therapy. To assess whether the mutation was constitutive or somatic in nature, we evaluated its presence analyzing either the neoplastic or normal cell population (epidermal cells or CD3-positive T lymphocytes). KITM541L substitution was found in 4 out of 5 patients and in all it was somatic in nature. All patients were treated with low dose imatinib (100 mg daily orally), achieving complete and persistent clinical and hematological remission (median follow-up 74 months). One patient relapsed after 50 months. Our study strongly suggests to search for the KITM541L in patients with CEL, NOS, negative for PDGFRalpha and PDGFRbeta abnormalities, to identify a subgroup of cases who may benefit from low dose imatinib therapy.
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Affiliation(s)
- Alessandra Iurlo
- Hematology and Transplantation Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico and University of Milan, Milan, Italy; Oncohematology Unit of the Elderly, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico and University of Milan, Milan, Italy
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Ho CF, Chan KW, Yang WC, Chiang YC, Chung YT, Kuo J, Wang CY. Development of a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction assay for the differential diagnosis of Feline leukemia virus vaccine and wild strains. J Vet Diagn Invest 2014; 26:496-506. [DOI: 10.1177/1040638714534850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A multiplex amplification refractory mutation system reverse transcription polymerase chain reaction (ARMS RT-PCR) was developed for the differential diagnosis of Feline leukemia virus (FeLV) vaccine and wild-type strains based on a point mutation between the vaccine strain (S) and the wild-type strain (T) located in the p27 gene. This system was further upgraded to obtain a real-time ARMS RT-PCR (ARMS qRT-PCR) with a high-resolution melt analysis (HRMA) platform. The genotyping of various strains of FeLV was determined by comparing the HRMA curves with the defined wild-type FeLV (strain TW1), and the results were expressed as a percentage confidence. The detection limits of ARMS RT-PCR and ARMS qRT-PCR combined with HRMA were 100 and 1 copies of transcribed FeLV RNA per 0.5 ml of sample, respectively. No false-positive results were obtained with 6 unrelated pathogens and 1 feline cell line. Twelve FeLV Taiwan strains were correctly identified using ARMS qRT-PCR combined with HRMA. The genotypes of the strains matched the defined FeLV wild-type strain genotype with at least 91.17% confidence. A higher degree of sequence polymorphism was found throughout the p27 gene compared with the long terminal repeat region. In conclusion, the current study describes the phylogenetic relationship of the FeLV Taiwan strains and demonstrates that the developed ARMS RT-PCR assay is able to be used to detect the replication of a vaccine strain that has not been properly inactivated, thus acting as a safety check for the quality of FeLV vaccines.
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Affiliation(s)
- Chia-Fang Ho
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan (Ho, Chung, Kuo, Wang)
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan, Yang)
- Department of Biological Sciences, College of Science, National Sun Yat-sen University, Kaoshiung, Taiwan (Chiang)
| | - Kun-Wei Chan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan (Ho, Chung, Kuo, Wang)
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan, Yang)
- Department of Biological Sciences, College of Science, National Sun Yat-sen University, Kaoshiung, Taiwan (Chiang)
| | - Wei-Cheng Yang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan (Ho, Chung, Kuo, Wang)
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan, Yang)
- Department of Biological Sciences, College of Science, National Sun Yat-sen University, Kaoshiung, Taiwan (Chiang)
| | - Yu-Chung Chiang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan (Ho, Chung, Kuo, Wang)
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan, Yang)
- Department of Biological Sciences, College of Science, National Sun Yat-sen University, Kaoshiung, Taiwan (Chiang)
| | - Yang-Tsung Chung
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan (Ho, Chung, Kuo, Wang)
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan, Yang)
- Department of Biological Sciences, College of Science, National Sun Yat-sen University, Kaoshiung, Taiwan (Chiang)
| | - James Kuo
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan (Ho, Chung, Kuo, Wang)
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan, Yang)
- Department of Biological Sciences, College of Science, National Sun Yat-sen University, Kaoshiung, Taiwan (Chiang)
| | - Chi-Young Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan (Ho, Chung, Kuo, Wang)
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan, Yang)
- Department of Biological Sciences, College of Science, National Sun Yat-sen University, Kaoshiung, Taiwan (Chiang)
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Semerci CN, Kalay E, Yıldırım C, Dinçer T, Olmez A, Toraman B, Koçyiğit A, Bulgu Y, Okur V, Satıroğlu-Tufan L, Akarsu NA. Novel splice-site and missense mutations in the ALDH1A3 gene underlying autosomal recessive anophthalmia/microphthalmia. Br J Ophthalmol 2014; 98:832-40. [PMID: 24568872 DOI: 10.1136/bjophthalmol-2013-304058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIM This study aimed to identify the underlying genetic defect responsible for anophthalmia/microphthalmia. METHODS In total, two Turkish families with a total of nine affected individuals were included in the study. Affymetrix 250 K single nucleotide polymorphism genotyping and homozygosity mapping were used to identify the localisation of the genetic defect in question. Coding region of the ALDH1A3 gene was screened via direct sequencing. cDNA samples were generated from primary fibroblast cell cultures for expression analysis. Reverse transcriptase PCR (RT-PCR) analysis was performed using direct sequencing of the obtained fragments. RESULTS The causative genetic defect was mapped to chromosome 15q26.3. A homozygous G>A substitution (c.666G>A) at the last nucleotide of exon 6 in the ALDH1A3 gene was identified in the first family. Further cDNA sequencing of ALDH1A3 showed that the c.666G>A mutation caused skipping of exon 6, which predicted in-frame loss of 43 amino acids (p.Trp180_Glu222del). A novel missense c.1398C>A mutation in exon 12 of ALDH1A3 that causes the substitution of a conserved asparagine by lysine at amino acid position 466 (p.Asn466Lys) was observed in the second family. No extraocular findings-except for nevus flammeus in one affected individual and a variant of Dandy-Walker malformation in another affected individual-were observed. Autistic-like behaviour and mental retardation were observed in three cases. CONCLUSIONS In conclusion, novel ALDH1A3 mutations identified in the present study confirm the pivotal role of ALDH1A3 in human eye development. Autistic features, previously reported as an associated finding, were considered to be the result of social deprivation and inadequate parenting during early infancy in the presented families.
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Affiliation(s)
- C Nur Semerci
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Ersan Kalay
- Department of Medical Biology, School of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Cem Yıldırım
- Department of Ophthalmology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Tuba Dinçer
- Department of Medical Biology, School of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Akgün Olmez
- Department of Pediatric Neurology, Denizli State Hospital of Ministry of Health, Denizli, Turkey
| | - Bayram Toraman
- Department of Medical Biology, School of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Ali Koçyiğit
- Department of Radiology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Yunus Bulgu
- Department of Ophthalmology, State Hospital, Şuhut-Afyonkarahisar, Afyon, Turkey
| | - Volkan Okur
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Lale Satıroğlu-Tufan
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Nurten A Akarsu
- Department of Medical Genetics, Gene Mapping Laboratory, School of Medicine, Hacettepe University, Ankara, Turkey
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Abstract
Over the last few years, several initiatives have described efforts to combine previously invented techniques in molecular biology with parallel detection principles to sequence or genotype DNA signatures. The Infinium system from Illumina and the Affymetrix GeneChips are two systems suitable for whole-genome scoring of variable positions. However, directed candidate-gene approaches are more cost effective and several academic groups and the private sector provide techniques with moderate typing throughput combined with large sample capacity suiting these needs. Recently, whole-genome sequencing platforms based on the sequencing-by-synthesis principle were presented by 454 Life Sciences and Solexa, showing great potential as alternatives to conventional genotyping approaches. In addition to these sequencing initiatives, many efforts are pursuing novel ideas to facilitate fast and cost-effective whole genome sequencing, such as ligation-based sequencing. Reliable methods for routine re-sequencing of human genomes as a tool for personalized medicine, however, remain to be developed.
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Affiliation(s)
- Max Käller
- AlbaNova University Center, School of Biotechnology, Department of Gene Technology, Royal Institute of Technology, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.
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Curti MLR, Rogero MM, Baltar VT, Barros CR, Siqueira-Catania A, Ferreira SRG. FTO T/A and peroxisome proliferator-activated receptor-γ Pro12Ala polymorphisms but not ApoA1 -75 are associated with better response to lifestyle intervention in Brazilians at high cardiometabolic risk. Metab Syndr Relat Disord 2013; 11:169-76. [PMID: 23438152 DOI: 10.1089/met.2012.0055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The role of obesity-related polymorphisms on weight loss and inflammatory responses to interventions is unclear. We investigated associations of certain polymorphisms with response to a lifestyle intervention. METHODS This 9-month intervention on diet and physical activity included 180 Brazilians at high cardiometabolic risk, genotyped for the fat mass and obesity-associated (FTO) T/A, peroxisome proliferator-activated receptor-γ (PPARγ) Pro12Ala, and ApoA1 -75G/A polymorphisms. Changes in metabolic and inflammatory variables were analyzed according to these polymorphisms. RESULTS The intervention resulted in lower energy intake and higher physical activity. Anthropometric measurements, 2-hr plasma glucose, insulin, high-density lipoprotein cholesterol (HDL-C), and apolipoprotein B (ApoB) improved significantly for the total sample, and these benefits were similar among genotypes. Only variant allele carriers of FTO T/A decreased fasting plasma glucose after intervention (99.9±1.3 to 95.6±1.4 mg/dL, P=0.021). Mean blood pressure reduced after intervention in variant allele carriers of the PPARγ Pro12Ala (109.4±2.1 to 101.3±2.1 mmHg, P<0.001). Improvement in lipid variables was not significant after adjustment for medication. Only the reference genotype of PPARγ Pro12Ala increased apolipoprotein A1 (ApoA1) after intervention (134.3±2.4 to 140.6±2.3 mg/dL, P<0.001). Only variant allele carriers of FTO reduced C-reactive protein (CRP) concentration (0.366±0.031 to 0.286±0.029 mg/dL, P=0.023). CONCLUSION In Brazilian individuals, the FTO T/A polymorphism induces a favorable impact on inflammatory status and glucose metabolism. The reference genotype of PPARγ Pro12Ala seems to favor a better lipid profile, while the variant allele decreases blood pressure. Our data did not support benefits of the variant allele of ApoA1 -75G/A polymorphism. Further studies are needed to direct lifestyle intervention to subsets of individuals at cardiometabolic risk.
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Affiliation(s)
- Maira L R Curti
- Department of Nutrition, School of Public Health, University of Sao Paulo, Sao Paulo, Brazil
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Daher M, Costa FMM, Neves FAR. Genotyping the Mu-Opioid Receptor A118G Polymorphism Using the Real-time Amplification Refractory Mutation System: Allele Frequency Distribution Among Brazilians. Pain Pract 2013; 13:614-20. [DOI: 10.1111/papr.12042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/22/2013] [Indexed: 02/06/2023]
Affiliation(s)
- Mauricio Daher
- Department of Anesthesiology, University Hospital of Brasilia, University of Brasilia, Brasilia, Brazil
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Curti MLR, Pires MM, Barros CR, Siqueira-Catania A, Rogero MM, Ferreira SRG. Associations of the TNF-alpha -308 G/A, IL6 -174 G/C and AdipoQ 45 T/G polymorphisms with inflammatory and metabolic responses to lifestyle intervention in Brazilians at high cardiometabolic risk. Diabetol Metab Syndr 2012; 4:49. [PMID: 23176569 PMCID: PMC3527217 DOI: 10.1186/1758-5996-4-49] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/11/2012] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED BACKGROUND Cytokines secreted by the adipose tissue influence inflammation and insulin sensitivity, and lead to metabolic disturbances. How certain single-nucleotide polymorphisms (SNPs) interfere on lifestyle interventions is unclear. We assessed associations of selected SNPs with changes induced by a lifestyle intervention. METHODS This 9-month intervention on diet and physical activity included 180 Brazilians at high cardiometabolic risk, genotyped for the TNF-α -308 G/A, IL-6 -174 G/C and AdipoQ 45 T/G SNPs. Changes in metabolic and inflammatory variables were analyzed according to these SNPs. Individuals with at least one variant allele were grouped and compared with those with the reference genotype. RESULTS In the entire sample (66.7% women; mean age 56.5 ± 11.6 years), intervention resulted in lower energy intake, higher physical activity, and improvement in anthropometry, plasma glucose, HOMA-IR, lipid profile and inflammatory markers, except for IL-6 concentrations. After intervention, only variant allele carriers of the TNF-α -308 G/A decreased plasma glucose, after adjusting for age and gender (OR 2.96, p = 0.025). Regarding the IL6 -174 G/C SNP, carriers of the variant allele had a better response of lipid profile and adiponectin concentration, but only the reference genotype group decreased plasma glucose. In contrast to individuals with the reference genotype, carriers of variant allele of AdipoQ 45 T/G SNP did not change plasma glucose, apolipoprotein B, HDL-c and adiponectin concentrations in response to intervention. CONCLUSION The TNFα -308 G/A SNP may predispose a better response of glucose metabolism to lifestyle intervention. The IL-6 -174 G/C SNP may confer a beneficial effect on lipid but not on glucose metabolism. Our findings reinforce unfavorable effects of the AdipoQ 45 T/G SNP in lipid profile and glucose metabolism after intervention in Brazilians at cardiometabolic risk. Further studies are needed to direct lifestyle intervention to subsets of individuals at cardiometabolic risk.
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Affiliation(s)
- Maira LR Curti
- Department of Nutrition, School of Public Health, University of Sao Paulo, Av. Dr. Arnaldo, São Paulo, SP, 715, Brasil
| | - Milena M Pires
- Department of Nutrition, School of Public Health, University of Sao Paulo, Av. Dr. Arnaldo, São Paulo, SP, 715, Brasil
| | - Camila R Barros
- Department of Nutrition, School of Public Health, University of Sao Paulo, Av. Dr. Arnaldo, São Paulo, SP, 715, Brasil
| | - Antonela Siqueira-Catania
- Department of Nutrition, School of Public Health, University of Sao Paulo, Av. Dr. Arnaldo, São Paulo, SP, 715, Brasil
| | - Marcelo Macedo Rogero
- Department of Nutrition, School of Public Health, University of Sao Paulo, Av. Dr. Arnaldo, São Paulo, SP, 715, Brasil
| | - Sandra RG Ferreira
- Department of Nutrition, School of Public Health, University of Sao Paulo, Av. Dr. Arnaldo, São Paulo, SP, 715, Brasil
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Paux E, Sourdille P, Mackay I, Feuillet C. Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 2011; 30:1071-88. [PMID: 21989506 DOI: 10.1016/j.biotechadv.2011.09.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 08/24/2011] [Accepted: 09/25/2011] [Indexed: 01/04/2023]
Abstract
In the past two decades, the wheat community has made remarkable progress in developing molecular resources for breeding. A wide variety of molecular tools has been established to accelerate genetic and physical mapping for facilitating the efficient identification of molecular markers linked to genes and QTL of agronomic interest. Already, wheat breeders are benefiting from a wide range of techniques to follow the introgression of the most favorable alleles in elite material and develop improved varieties. Breeders soon will be able to take advantage of new technological developments based on Next Generation Sequencing. In this paper, we review the molecular toolbox available to wheat scientists and breeders for performing fundamental genomic studies and breeding. Special emphasis is given on the production and detection of single nucleotide polymorphisms (SNPs) that should enable a step change in saturating the wheat genome for more efficient genetic studies and for the development of new selection methods. The perspectives offered by the access to an ordered full genome sequence for further marker development and enhanced precision breeding is also discussed. Finally, we discuss the advantages and limitations of marker-assisted selection for supporting wheat improvement.
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Affiliation(s)
- Etienne Paux
- INRA-UBP 1095, Genetics Diversity and Ecophysiology of Cereals, 234 Avenue du Brézet, Clermont-Ferrand, France
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Woodrow P, Pontecorvo G, Ciarmiello LF. Isolation of Ty1-copia retrotransposon in myrtle genome and development of S-SAP molecular marker. Mol Biol Rep 2011; 39:3409-18. [PMID: 21725640 DOI: 10.1007/s11033-011-1112-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/17/2011] [Indexed: 01/22/2023]
Abstract
Long terminal repeat (LTR)-retrotransposons are mobile genetic elements that are ubiquitous in plants and constitute a major portion of their nuclear genomes. LTR- retrotransposons possess unique properties that make them appropriate for investigating relationships between populations, varieties and closely related species. Myrtus communis L. is an evergreen shrub growing spontaneously throughout the Mediterranean area. Accessions show significant variations for agriculturally important traits, so the development of specific molecular markers for conservation and characterization of myrtle germplasm is desirable to conserve biodiversity. In this study, we isolated the first retrotransposon Ty1-copia-like element (Tmc1) in Myrtus communis L. genome and used this as a molecular marker. We successfully employed the S-SAP marker system to specifically characterize four myrtle accessions belonging to different areas in the province of Caserta (Italy). The high level of polymorphism detected in isolated LTRs, make Tmc1 a good molecular marker for this species. Our findings confirm that retrotransposon-based molecular markers are particularly valuable tools for plant molecular characterization studies.
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Affiliation(s)
- Pasqualina Woodrow
- Department of Life Science, II University of Naples, Via Vivaldi, 43, 81100, Caserta, Italy
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Lee YJ, Chen HY, Wong ML, Hsu WL. Molecular detection of autosomal-dominant feline polycystic kidney disease by multiplex amplification refractory mutation system polymerase chain reaction. J Vet Diagn Invest 2010; 22:424-8. [PMID: 20453219 DOI: 10.1177/104063871002200314] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Feline autosomal-dominant polycystic kidney disease (ADPKD), with its characteristic growth of fluid-filled cysts of different sizes, is the most prevalent inherited genetic disease of cats. The point mutation (C-->A transversion) in exon 29 of the PKD1 gene is known to contribute to ADPKD development and can thus serve as a target for the molecular genetic diagnosis of ADPKD. To this end, a simple amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) was designed with 3 primers: 2 forward primers specifically targeting either the mutant or normal allele, and 1 universal reverse primer for amplification of both alleles. The new method was tested on the DNA from 35 feline blood samples, which included 15 mutant cats and 20 wild type cats. As verified by direct DNA sequencing, both sensitivity and specificity of this tri-primer ARMS PCR were 100%. As the multiplex ARMS PCR test can be performed in a single PCR reaction without other post-PCR procedures, it is a simple and accurate method for molecular studies of feline ADPKD.
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Affiliation(s)
- Ya-Jane Lee
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung-Hsing University, Taichung 402, Taiwan
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Van Borm S, Ferreira HL, van den Berg T. Fine quantification of avian influenza H5N1 escape mutant quasispecies populations using mutation-specific real-time PCR. Avian Dis 2010; 54:558-64. [PMID: 20521694 DOI: 10.1637/8756-033109-resnote.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Influenza viruses have a rapid replication cycle, using enzymes without proofreading capacity and generating multiple virus quasispecies during replication. The identification and quantification of these quasispecies populations require time-consuming and expensive cloning and sequencing approaches. In the present study, we developed mutation-specific real-time PCR (RT-PCR) tests for the fine quantification of mutations in a background of wild-type sequences. As a proof-of-concept model, we developed mutation-specific RT-PCR tests to quantify antibody escape mutations during passage under monoclonal antibody (mAb) selection pressure in quasispecies populations of HPAI A/crested eagle/Belgium/01/2004 (H5N1). Mutation-specific RT-PCRs were developed for two mutations (one in HA1 and one in HA2) and validated using plasmids representing either the wildtype sequence or the mutation. The approach achieves a precise and accurate estimation of mutation frequencies on mixed populations in the range of 1% to 99% and does not require standard curves or calibrators. For the HA1 mutations, a directional increase of % G over the passages towards fixation of the G mutation could be observed. On the contrary, as expected from the inaccessibility of the HA2 region to antibodies, the HA2 mutation increased in frequency by factors unrelated to mAb-driven selection. This approach allows in-depth analysis of quasispecies dynamics using large sample sizes. It may also be applied to the dynamics of hot spots of mutations in several genes, such as HA or PB2, and to the early detection of critical changes in the field situation.
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Affiliation(s)
- Steven Van Borm
- Veterinary and Agrochemical Research Center, Groeselenberg 99, 1180 Ukkel, Belgium.
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A PCR based SNPs marker for specific characterization of English walnut (Juglans regia L.) cultivars. Mol Biol Rep 2010; 38:1237-49. [PMID: 20577817 DOI: 10.1007/s11033-010-0223-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 06/11/2010] [Indexed: 10/19/2022]
Abstract
English walnut (Juglans regia L.) is the most economically important species from all the 21 species belonging to the genus Juglans and is an important and healthy food as well as base material for timber industry. The aim of this study was to develop a simple technique for specific characterization of English walnut using DNA method. The first and second internal transcribed spacers (ITS1 and ITS2) as well as the intervening 5.8S coding region of the rRNA gene for 18 cultivars of J. regia L. isolated from different geographic origins were characterized. The size of the spacers sequences ranged from 257 to 263 bases for ITS1 and from 217 to 219 bases for ITS2. Variation of GC contents has also been observed and scored as 55-56.7 and 57.1-58.9% for ITS1 and ITS2, respectively. This data exhibited the presence of polymorphism among cultivars. Alignment of the ITS1-5.8S-ITS2 sequences from 18 walnut cultivars showed that there were 244 single nucleotide polymorphisms (SNPs) and 1 short insertion-deletion (indel) at 5' end ITS1. Amplification refractory mutation system strategy was successfully applied to the SNP markers of the ITS1 and ITS2 sequences for the fingerprinting analysis of 17 on 18 walnut cultivars. The prediction of ITS1 and ITS2 RNA secondary structure from each cultivar was improved by detecting key functional elements shared by all sequences in the alignments. Phylogenetic analysis of the ITS1-5.8S-ITS2 region clearly separated the isolated sequences into two clusters. The results showed that ITS1 and ITS2 region could be used to discriminate these walnut cultivars.
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Chulakasian S, Lee MS, Wang CY, Chiou SS, Lin KH, Lin FY, Hsu TH, Wong ML, Chang TJ, Hsu WL. Multiplex Amplification Refractory Mutation System Polymerase Chain Reaction (ARMS-PCR) for diagnosis of natural infection with canine distemper virus. Virol J 2010; 7:122. [PMID: 20534175 PMCID: PMC2907576 DOI: 10.1186/1743-422x-7-122] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/10/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Canine distemper virus (CDV) is present worldwide and produces a lethal systemic infection of wild and domestic Canidae. Pre-existing antibodies acquired from vaccination or previous CDV infection might interfere the interpretation of a serologic diagnosis method. In addition, due to the high similarity of nucleic acid sequences between wild-type CDV and the new vaccine strain, current PCR derived methods cannot be applied for the definite confirmation of CD infection. Hence, it is worthy of developing a simple and rapid nucleotide-based assay for differentiation of wild-type CDV which is a cause of disease from attenuated CDVs after vaccination. High frequency variations have been found in the region spanning from the 3'-untranslated region (UTR) of the matrix (M) gene to the fusion (F) gene (designated M-F UTR) in a few CDV strains. To establish a differential diagnosis assay, an amplification refractory mutation analysis was established based on the highly variable region on M-F UTR and F regions. RESULTS Sequences of frequent polymorphisms were found scattered throughout the M-F UTR region; the identity of nucleic acid between local strains and vaccine strains ranged from 82.5% to 93.8%. A track of AAA residue located 35 nucleotides downstream from F gene start codon highly conserved in three vaccine strains were replaced with TGC in the local strains; that severed as target sequences for deign of discrimination primers. The method established in the present study successfully differentiated seven Taiwanese CDV field isolates, all belonging to the Asia-1 lineage, from vaccine strains. CONCLUSIONS The method described herein would be useful for several clinical applications, such as confirmation of nature CDV infection, evaluation of vaccination status and verification of the circulating viral genotypes.
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Affiliation(s)
- Songkhla Chulakasian
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, 250 Kou Kuang Road, Taichung 402, Taiwan
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Liu X, Law HY, Tan YM, Hong Y. High-throughput beta-thalassemia carrier screening by allele-specific Q-primer real-time polymerase chain reaction. Anal Biochem 2010; 404:97-9. [PMID: 20433808 DOI: 10.1016/j.ab.2010.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 04/21/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
Abstract
Based on a novel Q-primer real-time polymerase chain reaction (PCR) system, we designed allele-specific Q-primers for the detection of three beta-thalassemia mutations [Cd41/42(-TCTT), IVSI nt5 (G>C), and IVSII nt654 (C>T)] that have a high carrier frequency in Southeast Asia. With clear distinction between heterozygote and wild-type, DeltaC(t) (threshold cycle) values were defined. The results of evaluating 139 blinded samples by our system match perfectly with those obtained by the conventional reverse dot blot (RDB) method. With a 384-well plate that included replicates in the same analysis, our throughput reached 190 reactions per run with a turnaround time as short as 130 min, and the cost of consumables was as low as $1 (US) for each test.
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23
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Enhancing allele-specific PCR for specifically detecting short deletion and insertion DNA mutations. Mol Cell Probes 2010; 24:15-9. [DOI: 10.1016/j.mcp.2009.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/29/2009] [Accepted: 08/02/2009] [Indexed: 11/23/2022]
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Pinheiro H, Bordeira-Carriço R, Seixas S, Carvalho J, Senz J, Oliveira P, Inácio P, Gusmão L, Rocha J, Huntsman D, Seruca R, Oliveira C. Allele-specific CDH1 downregulation and hereditary diffuse gastric cancer. Hum Mol Genet 2009; 19:943-52. [PMID: 19965908 DOI: 10.1093/hmg/ddp537] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hereditary diffuse gastric cancer (HDGC) is an autosomal dominant cancer susceptibility syndrome characterized by early-onset diffuse gastric cancer (DGC) and lobular breast cancer. E-cadherin (CDH1) heterozygous germline mutations and deletions are found in 40% of families. Independent of CDH1 alterations, most HDGC tumours display mislocalized or absent E-cadherin immunoexpression, therefore undetected defects at the CDH1 locus may still be involved. We aimed at determining whether CDH1 mutation-negative probands display germline CDH1 allele-specific expression (ASE) imbalance, using a single-nucleotide primer extension-based procedure and tried to uncover the underlying molecular defect. CDH1 ASE analysis was performed using three intragenic SNPs in RNA extracted from the blood of 21 cancer-free individuals and 22 HDGC probands (5 CDH1 mutation carriers and 17 CDH1 negative). Germline promoter methylation, deletions and haplotype-related susceptibility at the CDH1 locus were analysed. Both CDH1 alleles from cancer-free individuals displayed equivalent expression levels, whereas monoallelic CDH1 expression or high allelic expression imbalance (AI) was present in 80% of CDH1 mutant and 70.6% (n = 12) of CDH1-negative HDGC probands. Germline deletions and promoter hypermethylation were found in 25% of probands displaying high CDH1 AI. No particular haplotype was found to be associated with CDH1 high AI. Germline CDH1 AI is highly frequent among CDH1 mutation-negative probands but was not seen in cancer-free individuals. This implicates the CDH1 locus in the majority of mutation-negative HDGC families.
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Affiliation(s)
- Hugo Pinheiro
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto 4200-465, Portugal
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Gineikiene E, Stoskus M, Griskevicius L. Single nucleotide polymorphism-based system improves the applicability of quantitative PCR for chimerism monitoring. J Mol Diagn 2008; 11:66-74. [PMID: 19056844 DOI: 10.2353/jmoldx.2009.080039] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, several studies demonstrated the feasibility of a real-time quantitative PCR (qPCR) approach for chimerism monitoring. qPCR offers a fast, sensitive, and elegant quantification of genotypes. However, before it becomes an established method for routine chimerism monitoring, a qPCR marker set for every transplant pair should be available. This requirement poses a major challenge since the genetic markers for qPCR--short insertions/deletions (Indels) and single nucleotide polymorphisms (SNPs)--published to-date do not guarantee applicability for every transplant pair. The aim of our study was to design and validate a new SNP allele-specific system to supplement an already existing Indel primer panel and improve applicability of the qPCR approach for chimerism status monitoring. Here, we present an approach for an economical in-house design of SNP allele-specific qPCR primers/probe sets with a locus-individualized reference system that allows for the accurate quantification of the respective informative locus using a simple DeltaDeltaCt method. We designed primers/probe sets specific for seven biallelic SNP loci and validated them in a population of 30 transplant pairs. Repeatability varied depending on the amount of quantifiable genotype. The combination of our SNP-qPCR system and Indel primers increased recipient genotype identification from 86.6% to 96.6% when tested in a population of our transplant pairs. These results demonstrate the feasibility of our SNP-based qPCR approach to improve the applicability of a qPCR for chimerism monitoring.
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Affiliation(s)
- Egle Gineikiene
- Hematology, Oncology, and Transfusion Medicine Center, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania.
| | - Mindaugas Stoskus
- Hematology, Oncology, and Transfusion Medicine Center, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania
| | - Laimonas Griskevicius
- Hematology, Oncology, and Transfusion Medicine Center, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania; Clinics of Internal, Family Medicine, and Oncology, Vilnius University, Vilnius, Lithuania
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Abstract
Insects comprise the largest species composition in the entire animal kingdom and possess a vast undiscovered genetic diversity and gene pool that can be better explored using molecular marker techniques. Current trends of application of DNA marker techniques in diverse domains of insect ecological studies show that mitochondrial DNA (mtDNA), microsatellites, random amplified polymorphic DNA (RAPD), expressed sequence tags (EST) and amplified fragment length polymorphism (AFLP) markers have contributed significantly for progresses towards understanding genetic basis of insect diversity and for mapping medically and agriculturally important genes and quantitative trait loci in insect pests. Apart from these popular marker systems, other novel approaches including transposon display, sequence-specific amplification polymorphism (S-SAP), repeat-associated polymerase chain reaction (PCR) markers have been identified as alternate marker systems in insect studies. Besides, whole genome microarray and single nucleotide polymorphism (SNP) assays are becoming more popular to screen genome-wide polymorphisms in fast and cost effective manner. However, use of such methodologies has not gained widespread popularity in entomological studies. The current study highlights the recent trends of applications of molecular markers in insect studies and explores the technological advancements in molecular marker tools and modern high throughput genotyping methodologies that may be applied in entomological researches for better understanding of insect ecology at molecular level.
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Affiliation(s)
- Susanta K Behura
- Department of Entomology, 505 S Goodwin Avenue, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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Ghebranious N, Mallum J. A Single multiplexed allele-specific polymerase chain reaction for simultaneous detection of alpha1-antitrypsin S and Z mutations. ACTA ACUST UNITED AC 2006; 9:185-9. [PMID: 16225408 DOI: 10.1089/gte.2005.9.185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Alpha1-antitrypsin (AAT) deficiency is an inherited disorder that can cause lung disease in adults and liver disease in adults and children. The S and Z mutations are the two most common mutations found in the AAT-deficient patients. We have developed a simple multiplexed allele-specific-PCR to detect both the S and Z mutations and the corresponding wild-type alleles. Polymerase chain reaction (PCR) product could be resolved on an agarose gel or using any fluorescent gel detection system. We obtained accurate genotyping results for the four alleles; the S, Z, and their corresponding wild-type alleles for all investigated samples simultaneously. The approach described in this paper is rapid, cost effective, and reliable and can also be adaptable into any laboratory setting because of its simplicity.
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Affiliation(s)
- Nader Ghebranious
- Molecular Diagnostics Genotyping Laboratory, Marshfield Clinic, Marshfield, Wisconsin 54449, USA.
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Wechsler ME, Lehman E, Lazarus SC, Lemanske RF, Boushey HA, Deykin A, Fahy JV, Sorkness CA, Chinchilli VM, Craig TJ, DiMango E, Kraft M, Leone F, Martin RJ, Peters SP, Szefler SJ, Liu W, Israel E. beta-Adrenergic receptor polymorphisms and response to salmeterol. Am J Respir Crit Care Med 2005; 173:519-26. [PMID: 16322642 PMCID: PMC2662935 DOI: 10.1164/rccm.200509-1519oc] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Several studies suggest that patients with asthma who are homozygous for arginine at the 16th position of the beta2-adrenergic receptor may not benefit from short-acting beta-agonists. OBJECTIVES We investigated whether such genotype-specific effects occur when patients are treated with long-acting beta-agonists and whether such effects are modified by concurrent inhaled corticosteroid (ICS) use. METHODS We compared salmeterol response in patients with asthma homozygous for arginine at B16 (B16Arg/Arg) with those homozygous for glycine at B16 (B16Gly/Gly) in two separate cohorts. In the first, subjects were randomized to regular therapy with salmeterol while simultaneously discontinuing ICS therapy. In the second, subjects were randomized to regular therapy with salmeterol while continuing concomitant ICS. RESULTS In both trials, B16Arg/Arg subjects did not benefit compared with B16Gly/Gly subjects after salmeterol was initiated. In the first cohort, compared with placebo, the addition of salmeterol was associated with a 51.4 L/min lower A.M. peak expiratory flow (PEF; p = 0.005) in B16Arg/Arg subjects(salmeterol, n = 12; placebo, n = 5) as compared with B16Gly/Gly subjects (salmeterol, n = 13; placebo, n = 13). In the second cohort, B16Arg/Arg subjects treated with salmeterol and ICS concurrently (n = 8) had a lower A.M. PEF (36.8 L/min difference, p = 0.048) than B16Gly/Gly subjects (n = 22) treated with the same regimen. In addition, B16 Arg/Arg subjects in the second cohort had lower FEV1 (0.42 L, p = 0.003), increased symptom scores (0.2 units, p = 0.034), and increased albuterol rescue use (0.95 puffs/d, p = 0.004) compared with B16Gly/Gly subjects. CONCLUSIONS Relative to B16Gly/Gly patients with asthma, B16Arg/Arg patients with asthma may have an impaired therapeutic response to salmeterol in either the absence or presence of concurrent ICS use. Investigation of alternate treatment strategies may benefit this group.
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Boniotto M, Segat L, Milanese M, Crovella S. Detection of two functional polymorphisms in the promoter region of the IL-18 gene by single-tube allele specific PCR and melting temperature analysis. J Immunol Methods 2005; 304:184-8. [PMID: 16111697 DOI: 10.1016/j.jim.2005.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 06/14/2005] [Accepted: 06/30/2005] [Indexed: 11/22/2022]
Abstract
IL-18 is an important cytokine in both innate and acquired immunity. IL-18 promoter polymorphisms have been investigated in several autoimmune and infectious diseases. Here we present two assays for a medium to a high throughput genotyping of C-607A and G-137C IL-18 SNPs. Using these protocols we have been able to rapidly genotype a cohort of 131 healthy Italian individuals. The assays, based on a multiplex allele-specific PCR and the melting temperature analysis of the PCR product, are rapid, easily automated, inexpensive and well suited to case-control association studies.
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Affiliation(s)
- Michele Boniotto
- Genetics Service, IRCCS Burlo Garofolo, Via dell'Istria 65/1, 34100 Trieste, Italy
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Kakihara F, Kurebayashi Y, Tojo Y, Tajima H, Hasegawa S, Yohda M. MagSNiPer: A new single nucleotide polymorphism typing method based on single base extension, magnetic separation, and chemiluminescence. Anal Biochem 2005; 341:77-82. [PMID: 15866530 DOI: 10.1016/j.ab.2005.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Indexed: 10/25/2022]
Abstract
We have developed a new method for typing single nucleotide polymorphisms (SNPs), MagSNiPer, based on single base extension, magnetic separation, and chemiluminescence. Single base nucleotide extension reaction is performed with a biotinylated primer whose 3' terminus is contiguous to the SNP site with a tag-labeled ddNTP. Then the primers are captured by magnetic-coated beads with streptavidin, and unincorporated labeled ddNTP is removed by magnetic separation. The magnetic beads are incubated with anti-tag antibody conjugated with alkaline phosphatase. After the removal of excess conjugates by magnetic separation, SNP typing is performed by measuring chemiluminescence. The incorporation of labeled ddNTP is monitored by chemiluminescence induced by alkaline phosphatase. MagSNiPer is a simple and robust SNP typing method with a wide dynamic range and high sensitivity. Using MagSNiPer, we could perform SNP typing with as little as 10(-17) mol of template DNA.
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Affiliation(s)
- Fumiko Kakihara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
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31
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Tojo Y, Asahina J, Miyashita Y, Takahashi M, Matsumoto N, Hasegawa S, Yohda M, Tajima H. Development of an automation system for single nucleotide polymorphisms genotyping using bio-strand, a new three-dimensional microarray. J Biosci Bioeng 2005; 99:120-4. [PMID: 16233767 DOI: 10.1263/jbb.99.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Accepted: 11/12/2004] [Indexed: 12/29/2022]
Abstract
Previously, we developed a novel three-dimensional microarray system called Bio-Strand, which may be used in various applications including single nucleotide polymorphisms genotyping. In Bio-Strand, samples for detection are immobilized on a one-dimensional thread, which is wound around a cylinder-shaped core to form a three-dimensional thread-and-core structure. The thread-and-core structure is then inserted into a plastic pipette tip, where hybridization and detection are performed. In this study, we have developed an automation system, NIAGALA Bio-Station SDx, which enables automated hybridization and detection during the genotyping procedure using Bio-Strand. Using this system, we have performed the single nucleotide polymorphism (SNP) genotyping of CYP2C, one of the important human cytochrome P450 genes and the results were completely consistent with the genotyping results determined by the TaqMan method.
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Affiliation(s)
- Yuriko Tojo
- Precision System Science Co., Ltd., 88 Kamihongo, Matsudo, Chiba 270-0025, Japan
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32
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Patrinos GP, Kollia P, Papadakis MN. Molecular diagnosis of inherited disorders: lessons from hemoglobinopathies. Hum Mutat 2005; 26:399-412. [PMID: 16138310 DOI: 10.1002/humu.20225] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hemoglobinopathies constitute a major health problem worldwide, with a high carrier frequency, particularly in certain regions where malaria has been endemic. These disorders are characterized by a vast clinical and hematological phenotypic heterogeneity. Over 1,200 different genetic alterations that affect the DNA sequence of the human alpha-like (HBZ, HBA2, HBA1, and HBQ1) and beta-like (HBE1, HBG2, HBG1, HBD, and HBB) globin genes are mainly responsible for the observed clinical heterogeneity. These mutations, together with detailed information about the resulting phenotype, are documented in the globin locus-specific HbVar database. Family studies and comprehensive hematological analyses provide useful insights for accurately diagnosing thalassemia at the DNA level. For this purpose, numerous techniques can provide accurate, rapid, and cost-effective identification of the underlying genetic defect in affected individuals. The aim of this article is to review the diverse methodological and technical platforms available for the molecular diagnosis of inherited disorders, using thalassemia and hemoglobinopathies as a model. This article also attempts to shed light on issues closely related to thalassemia diagnostics, such as prenatal and preimplantation genetic diagnoses and genetic counseling, for better-quality disease management.
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Affiliation(s)
- George P Patrinos
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, MGC-Department of Cell Biology and Genetics, Rotterdam, The Netherlands.
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33
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Tews B, Wilhelm J, Summerer D, Strerath M, Marx A, Friedhoff P, Pingoud A, Hahn M. Application of the C4'-alkylated deoxyribose primer system (CAPS) in allele-specific real-time PCR for increased selectivity in discrimination of single nucleotide sequence variants. Biol Chem 2004; 384:1533-41. [PMID: 14669997 DOI: 10.1515/bc.2003.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This study describes a quantitative real-time PCR-based approach for discrimination of single nucleotide sequence variants, called CAPS (C4' alkylated primer system). To increase the discrimination potential of DNA polymerases against competing sequence variants of single nucleotides, 3'-terminally modified primers were designed carrying a methyl residue bound to the C4' of the thymidylate deoxyribose. In a model sequence system positional dependencies of modified thymidylate (at -1, -2, -3) were tested for their influence on discrimination. Highest discrimination factors were obtained with the modification at the ultimate 3'-position. In a comparison between Taq and Pwo DNA polymerases, substantial better results were obtained by Taq DNA polymerase. In contrast to conventional PCR methods for discrimination of sequence variants, achieving a maximum discrimination potential of about 20, CAPS is capable of obtaining sequence-specific amplifications of a desired target among discriminated templates with a dynamic range of 1:100. Therefore, CAPS is a method able to quantitatively discriminate two sequence variants only differing in a single base (e.g., SNP alleles or point mutations). The range of applications of this easy to perform, fast and reliable technique reaches from medical diagnostics, transplantation medicine, molecular and cell biology to human genetics. Targeting of SNPs assures a universal exertion of this method, since these markers are gender-independent, highly abundant and ubiquitous.
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Affiliation(s)
- Björn Tews
- Institut für Biochemie, FB 08, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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Khan F, Agarwal A, Agrawal S. Significance of chimerism in hematopoietic stem cell transplantation: new variations on an old theme. Bone Marrow Transplant 2004; 34:1-12. [PMID: 15156163 DOI: 10.1038/sj.bmt.1704525] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The main goal of post-transplantation monitoring in hematopoietic stem cell transplantation (HSCT) is to predict negative events, such as disease relapse, graft rejection and graft-versus-host disease, in order to intervene with appropriate therapy. In this context, chimerism analysis is an important method in monitoring post HSCT outcome. Mixed chimerism (MC) is mainly evaluated to define engraftment and relapse. Detection of MC is a prerequisite in both myeloablative and nonmyeloablative HSCT, in order to assess the graft status and decide later therapeutic strategies such as donor lymphocyte infusion. In this review, we discuss various techniques including erythrocyte phenotyping, cytogenetic analysis, fluorescent in situ hybridization, restriction fragment length polymorphism, STR/VNTR analysis and real-time quantitative PCR, along with the various methods used to detect minimal residual disease (MRD) in different diseases such as chronic myeloid leukemia, acute myelomonocytic leukemia or acute lymphoblastic leukemia. The review mainly highlights the optimal methodological approach, which needs to be informative, sensitive and quantitatively accurate for MC detection. Future of post HSCT graft monitoring lies in the selection of the most accurate and sensitive technique to determine both MC and MRD. Such an approach would be helpful in not only determining relapse or rejection, but also in ascertaining various responses to different treatment modalities.
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Affiliation(s)
- F Khan
- Department of Medical Genetics, SGPGIMS, Lucknow, India
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35
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Russom A, Tooke N, Andersson H, Stemme G. Single nucleotide polymorphism analysis by allele-specific primer extension with real-time bioluminescence detection in a microfluidic device. J Chromatogr A 2004; 1014:37-45. [PMID: 14558610 DOI: 10.1016/s0021-9673(03)01033-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A microfluidic approach for rapid bioluminescent real-time detection of single nucleotide polymorphism (SNP) is presented. The method is based on single-step primer extension using pyrosequencing chemistry to monitor nucleotide incorporations in real-time. The method takes advantage of the fact that the reaction kinetics differ between matched and mismatched primer-template configurations. We show here that monitoring the initial reaction in real time accurately scores SNPs by comparing the initial reaction kinetics between matched and mismatched configurations. Thus, no additional treatment is required to improve the sequence specificity of the extension, which has been the case for many allele-specific extension assays. The microfluidic approach was evaluated using four SNPs. Three of the SNPs included primer-template configurations that have been previously reported to be difficult to resolve by allele-specific primer extension. All SNPs investigated were successfully scored. Using the microfluidic device, the volume for the bioluminescent assay was reduced dramatically, thus offering a cost-effective and fast SNP analysis method.
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Affiliation(s)
- Aman Russom
- Department of Signals, Sensors and Systems, Microsystem Technology, Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
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36
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Nesbit MA, Bowl MR, Harding B, Ali A, Ayala A, Crowe C, Dobbie A, Hampson G, Holdaway I, Levine MA, McWilliams R, Rigden S, Sampson J, Williams AJ, Thakker RV. Characterization of GATA3 Mutations in the Hypoparathyroidism, Deafness, and Renal Dysplasia (HDR) Syndrome. J Biol Chem 2004; 279:22624-34. [PMID: 14985365 DOI: 10.1074/jbc.m401797200] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome is an autosomal dominant disorder caused by mutations of the dual zinc finger transcription factor, GATA3. The C-terminal zinc finger (ZnF2) binds DNA, whereas the N-terminal finger (ZnF1) stabilizes this DNA binding and interacts with other zinc finger proteins, such as the Friends of GATA (FOG). We have investigated seven HDR probands and their families for GATA3 abnormalities and have identified two nonsense mutations (Glu-228 --> Stop and Arg-367 --> Stop); two intragenic deletions that result in frameshifts from codons 201 and 355 with premature terminations at codons 205 and 370, respectively; one acceptor splice site mutation that leads to a frameshift from codon 351 and a premature termination at codon 367; and two missense mutations (Cys-318 --> Arg and Asn-320 --> Lys). The functional effects of these mutations, together with a previously reported GATA3 ZnF1 mutation and seven other engineered ZnF1 mutations, were assessed by electrophoretic mobility shift, dissociation, yeast two-hybrid and glutathione S-transferase pull-down assays. Mutations involving GATA3 ZnF2 or adjacent basic amino acids resulted in a loss of DNA binding, but those of ZnF1 either lead to a loss of interaction with specific FOG2 ZnFs or altered DNA-binding affinity. These findings are consistent with the proposed three-dimensional model of ZnF1, which has separate DNA and protein binding surfaces. Thus, our results, which expand the spectrum of HDR-associated GATA3 mutations and report the first acceptor splice site mutation, help to elucidate the molecular mechanisms that alter the function of this zinc finger transcription factor and its role in causing this developmental anomaly.
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Affiliation(s)
- M Andrew Nesbit
- Nuffield Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford OX3 7LJ, United Kingdom
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37
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Klebs SHG, Hoffmann MW, Musholt PB, Bayer B, Musholt TJ. Detection of H-2 alleles by PCR-RFLP-an alternative to flow cytometry in the screening of transgenic mice. J Immunol Methods 2003; 276:197-205. [PMID: 12738373 DOI: 10.1016/s0022-1759(03)00063-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An increasing number of experimental models is based on well-defined transgenic mice in medical and biological research. Particularly in settings in which transgenic recombinants are used, a fast and reliable method is needed to screen for a defined H-2 background. For this purpose, flow cytometry with specific monoclonal antibodies is the standard procedure. However, epitopes of closely related rodent strains show only minor variations affecting the production of specific discriminating antibodies. Therefore, cross-reactivity of antibodies against specific major histocompatibility complex (MHC) leads to unreliable results in settings with closely related strains. In need of a method with high reliability, we have designed a screening assay based on polymerase chain reaction (PCR) followed by restriction fragment length polymorphisms (RFLP) to discriminate the MHC class I antigens H-2K(d), -K(b), -K(k), which are sequence variants of the H-2K gene. A part of the mus musculus MHC gene coding for H-2K-covering exons 4 and 5 with MHC-differentiating restriction sites-was amplified. Subsequent restriction digest of the PCR products allows to discriminate the three aforementioned alleles and to identify homozygous as well as heterozygous haplotypes. To distinguish transgenic mice defined by certain MHC backgrounds, the PCR-RFLP method is simple, cost-effective, specific, and reliable and can be used independently or in addition to other methods in any laboratory.
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Affiliation(s)
- Sven H G Klebs
- Department of Visceral and Transplantation Surgery & Clinical Chemistry, Hannover University Medical School, 30625, Hannover, Germany
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38
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Ahmadian A, Gharizadeh B, O'Meara D, Odeberg J, Lundeberg J. Genotyping by apyrase-mediated allele-specific extension. Nucleic Acids Res 2001; 29:E121. [PMID: 11812858 PMCID: PMC97629 DOI: 10.1093/nar/29.24.e121] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This report describes a single-step extension approach suitable for high-throughput single-nucleotide polymorphism typing applications. The method relies on extension of paired allele-specific primers and we demonstrate that the reaction kinetics were slower for mismatched configurations compared with matched configurations. In our approach we employ apyrase, a nucleotide degrading enzyme, to allow accurate discrimination between matched and mismatched primer-template configurations. This apyrase-mediated allele-specific extension (AMASE) protocol allows incorporation of nucleotides when the reaction kinetics are fast (matched 3'-end primer) but degrades the nucleotides before extension when the reaction kinetics are slow (mismatched 3'-end primer). Thus, AMASE circumvents the major limitation of previous allele-specific extension assays in which slow reaction kinetics will still give rise to extension products from mismatched 3'-end primers, hindering proper discrimination. It thus represents a significant improvement of the allele-extension method. AMASE was evaluated by a bioluminometric assay in which successful incorporation of unmodified nucleotides is monitored in real-time using an enzymatic cascade.
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Affiliation(s)
- A Ahmadian
- Center for Physics, Astronomy and Biotechnology, Department of Biotechnology, The Royal Institute of Technology (KTH), Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
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Israel E, Drazen JM, Liggett SB, Boushey HA, Cherniack RM, Chinchilli VM, Cooper DM, Fahy JV, Fish JE, Ford JG, Kraft M, Kunselman S, Lazarus SC, Lemanske RF, Martin RJ, McLean DE, Peters SP, Silverman EK, Sorkness CA, Szefler SJ, Weiss ST, Yandava CN. The effect of polymorphisms of the beta(2)-adrenergic receptor on the response to regular use of albuterol in asthma. Am J Respir Crit Care Med 2000; 162:75-80. [PMID: 10903223 DOI: 10.1164/ajrccm.162.1.9907092] [Citation(s) in RCA: 441] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Inhaled beta-adrenergic agonists are the most commonly used medications for the treatment of asthma although there is evidence that regular use may produce adverse effects in some patients. Polymorphisms of the beta(2)-adrenergic receptor (beta(2)-AR) can affect regulation of the receptor. Smaller studies examining the effects of such polymorphisms on the response to beta-agonist therapy have produced inconsistent results. We examined whether polymorphisms at codon 16 (beta(2)-AR-16) and codon 27 (beta(2)-AR-27) of the beta(2)-AR might affect the response to regular versus as-needed use of albuterol by genotyping the 190 asthmatics who had participated in a trial examining the effects of regular versus as needed albuterol use. During the 16-wk treatment period there was a small decline in morning peak expiratory flow in patients homozygous for arginine at B(2)-AR-16 (Arg/Arg) who used albuterol regularly. This effect was magnified during a 4-wk run out period, during which all patients returned to using as-needed albuterol, so that by the end of the study Arg Arg patients who had regularly used albuterol had a morning peak expiratory flow 30. 5 +/- 12.1 L/min lower (p = 0.012) than Arg/Arg patients who had used albuterol on an as needed basis. There was no decline in peak flow with regular use of albuterol in patients who were homozygous for glycine at beta(2)-AR-16. Evening peak expiratory flow also declined in the Arg/Arg patients who used albuterol regularly but not in those who used albuterol on an as-needed basis. No significant differences in outcomes between regular and as-needed treatment were associated with polymorphisms at position 27 of the beta(2)-AR. No other differences in asthma outcomes that we investigated occurred in relation to these beta(2)-AR polymorphisms. Polymorphisms of the beta(2)-AR may influence airway responses to regular inhaled beta-agonist treatment.
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Affiliation(s)
- E Israel
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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40
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Guttman A, Barta C, Szöke M, Sasvári-Székely M, Kalász H. Real-time detection of allele-specific polymerase chain reaction products by automated ultra-thin-layer agarose gel electrophoresis. J Chromatogr A 1998; 828:481-7. [PMID: 9916326 DOI: 10.1016/s0021-9673(98)00814-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Ultra-thin-layer agarose gel electrophoresis, a novel combination of agarose slab gel electrophoresis and capillary gel electrophoresis was introduced in conjunction with laser-induced fluorescence (LIF) scanning detection for the analysis of polymerase chain reaction (PCR) products. Allele-specific fragments, amplified from genomic DNA of patients with congenital adrenal hyperplasia (most often caused by mutations of 21-hydroxylase gene, CYP-21), were used as a model system to investigate the applicability, sensitivity and resolving power of the method. The allele-specific products were generated by PCR and separated by ultra-thin-layer agarose gel electrophoresis. The double-stranded DNA fragments were easily visualized in real-time via complexation during the separation process by the intercalator dye TO-PRO-3 which was part of the separation gel-buffer system. In this way, the migrating dsDNA-dye complexes were detected in real-time by a scanning LIF detection system with sub-nanogram sensitivity. The system employs a 632-nm solid-state laser and an avalanche photodiode detector scanning to the separation platform by means of a fiber bundle system. Automated ultra-thin-layer agarose gel electrophoresis with 'on the fly' TO-PRO-3 staining of dsDNA fragments and LIF detection system proved to be a very fast, high-throughput separation method for individual or multiplexed PCR products, with excellent sensitivity.
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Affiliation(s)
- A Guttman
- Genetic BioSystems Inc., San Diego, CA 92121, USA
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41
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Anwar R, Gallivan L, Miloszewski KJ, Markham AF. Splicing and missense mutations in the human FXIIIA gene causing FXIII deficiency: effects of these mutations on FXIIIA RNA processing and protein structure. Br J Haematol 1998; 103:425-8. [PMID: 9827915 DOI: 10.1046/j.1365-2141.1998.01017.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have investigated the molecular basis of factor XIII (FXIII) deficiency in a family from the north-west region of the U.K. and identified two sequence changes in the FXIII subunit A (FXIIIA) gene. We report a novel Asn to Lys mutation at codon 541, and a g-->a mutation at the intron 5/exon 6 splice junction in the FXIIIA gene. The splicing mutation results in two abnormal FXIIIA transcripts. The Asn541 residue is important for stabilizing an external fold in the FXIIIA barrel 1 domain. The Asn541Lys mutation is expected to result in inappropriate folding and therefore an unstable FXIIIA molecule.
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Affiliation(s)
- R Anwar
- Molecular Medicine Unit, University of Leeds, St James's University Hospital
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42
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Identification of a Large Deletion, Spanning Exons 4 to 11 of the Human Factor XIIIA Gene, in a Factor XIII-Deficient Family. Blood 1998. [DOI: 10.1182/blood.v91.1.149.149_149_153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Inherited deficiency of factor XIIIA subunit (FXIIIA) is an autosomal recessive disorder that is characterized by a life-long bleeding tendency and complications in wound healing. Molecular genetic studies have shown the deficiency can be due to small sequence changes within the FXIIIA gene, such as point mutations or microdeletions. On molecular analysis of the FXIIIA gene in an FXIII-deficient patient, of United Kingdom origin, we identified a putative homozygous missense mutation, Arg408Gln. However, the father of this patient is homozygous normal for arginine at codon 408. Having proved paternity in this pedigree by microsatellite analysis, we examined the FXIIIA RNA of the patient by reverse transcriptase-polymerase chain reaction and found the paternal allele to lack exons 4 through 11 inclusive. Hence, a huge deletion extending from intron 3 to intron 11 and the Arg408Gln mutation are jointly responsible for FXIIIA deficiency in this family. This is the first finding of such a large deletion in the FXIIIA gene.
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43
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Identification of a Large Deletion, Spanning Exons 4 to 11 of the Human Factor XIIIA Gene, in a Factor XIII-Deficient Family. Blood 1998. [DOI: 10.1182/blood.v91.1.149] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractInherited deficiency of factor XIIIA subunit (FXIIIA) is an autosomal recessive disorder that is characterized by a life-long bleeding tendency and complications in wound healing. Molecular genetic studies have shown the deficiency can be due to small sequence changes within the FXIIIA gene, such as point mutations or microdeletions. On molecular analysis of the FXIIIA gene in an FXIII-deficient patient, of United Kingdom origin, we identified a putative homozygous missense mutation, Arg408Gln. However, the father of this patient is homozygous normal for arginine at codon 408. Having proved paternity in this pedigree by microsatellite analysis, we examined the FXIIIA RNA of the patient by reverse transcriptase-polymerase chain reaction and found the paternal allele to lack exons 4 through 11 inclusive. Hence, a huge deletion extending from intron 3 to intron 11 and the Arg408Gln mutation are jointly responsible for FXIIIA deficiency in this family. This is the first finding of such a large deletion in the FXIIIA gene.
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Nzila-Mounda A, Mberu EK, Sibley CH, Plowe CV, Winstanley PA, Watkins WM. Kenyan Plasmodium falciparum field isolates: correlation between pyrimethamine and chlorcycloguanil activity in vitro and point mutations in the dihydrofolate reductase domain. Antimicrob Agents Chemother 1998; 42:164-9. [PMID: 9449279 PMCID: PMC105474 DOI: 10.1128/aac.42.1.164] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Sixty-nine Kenyan Plasmodium falciparum field isolates were tested in vitro against pyrimethamine (PM), chlorcycloguanil (CCG), sulfadoxine (SD), and dapsone (DDS), and their dihydrofolate reductase (DHFR) genotypes were determined. The in vitro data show that CCG is more potent than PM and that DDS is more potent than SD. DHFR genotype is correlated with PM and CCG drug response. Isolates can be classified into three distinct groups based on their 50% inhibitory concentrations (IC50s) for PM and CCG (P < 0.01) and their DHFR genotypes. The first group consists of wild-type isolates with mean PM and CCG IC50s of 3.71 +/- 6.94 and 0.24 +/- 0.21 nM, respectively. The second group includes parasites which all have mutations at codon 108 alone or also at codons 51 or 59 and represents one homogeneous group for which 25- and 6-fold increases in PM and CCG IC50s, respectively, are observed. Parasites with mutations at codons 108, 51, and 59 (triple mutants) form a third distinct group for which nine- and eightfold increases in IC50s, respectively, of PM and CCG compared to the second group are observed. Surprisingly, there is a significant decrease (P < 0.01) of SD and DDS susceptibility in these triple mutants. Our data show that more than 92% of Kenyan field isolates have undergone at least one point mutation associated with a decrease in PM activity. These findings are of great concern because they may indicate imminent PM-SD failure, and there is no affordable antimalarial drug to replace PM-SD (Fansidar).
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Affiliation(s)
- A Nzila-Mounda
- Wellcome Trust Research Laboratories, Kenya Medical Research Institute, Nairobi.
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45
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Anwar R, Puntis JW, Markham AF. A new mutation in the human lipoprotein lipase gene causing familial hyperchylomicronaemia. Mol Pathol 1997; 50:221-3. [PMID: 9350308 PMCID: PMC379631 DOI: 10.1136/mp.50.4.221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Lipoprotein lipase plays a major role in the regulation of lipid metabolism. The enzyme acts to hydrolyse triglycerides, providing free fatty acids for energy generation or storage, thus affecting the maturation of circulating lipoproteins. Biochemical and molecular analyses were performed on two siblings of consanguineous Pakistani origin, presenting with hyperchylomicronaemia, which revealed that the disorder resulted from lipoprotein lipase deficiency. Molecular analysis of the lipoprotein lipase gene has revealed a novel homozygous mutation, leucine to proline at amino acid residue 303, within the amino terminal domain of the protein.
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Affiliation(s)
- R Anwar
- Department of Medicine, University of Leeds, St James's University Hospital, UK
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Wang P, Brooks DR, Sims PF, Hyde JE. A mutation-specific PCR system to detect sequence variation in the dihydropteroate synthetase gene of Plasmodium falciparum. Mol Biochem Parasitol 1995; 71:115-25. [PMID: 7630375 DOI: 10.1016/0166-6851(95)00041-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Sulphur-based antimalarial drugs targeted at dihydropteroate synthetase (DHPS) are frequently used in synergistic combination with inhibitors of dihydrofolate reductase (DHFR) to combat chloroquine-resistant malaria. We have previously shown that lines of Plasmodium falciparum resistant to the most commonly used sulpha drug, sulphadoxine, carry point mutations in the DHPS coding region, relative to the sequence of sensitive strains (Brooks et al., Eur. J. Biochem. 224 (1994) 397-405). We have now developed PCR diagnostic assays based on allele-specific amplification that are able to detect such mutations. The four tests described can reliably discriminate all of the mutations observed to alter codons 436, 581 and 613, yielding allele-specific amplification products of different sizes in each case. Moreover, by careful adjustment of primer length and the degree of mismatch to target and non-target alleles, we were able to standardise all four tests to a single set of PCR conditions, allowing all possible mutations to be monitored simultaneously on one thermocycler. These assays should prove invaluable in further assessing the contribution of specific base changes in the DHPS gene of the parasite to the sulphadoxine resistance phenotype and to the clinical failure of the sulphadoxine/pyrimethamine combination Fansidar.
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Affiliation(s)
- P Wang
- Department of Biochemistry and Applied Molecular Biology, University of Manchester Institute of Science and Technology (UMIST), UK
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Wenham PR. DNA-based techniques in clinical biochemistry: a beginner's guide to theory and practice. Ann Clin Biochem 1992; 29 ( Pt 6):598-624. [PMID: 1489158 DOI: 10.1177/000456329202900602] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- P R Wenham
- Department of Clinical Biochemistry, Western General Hospital, Edinburgh, UK
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Abstract
Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is an autosomal recessive disorder which is known to cause Reye-like syndrome in children and sudden infant death. A point mutation of lysine329-to-glutamic acid329 substitution in the MCAD gene was recently identified as the most common mutation in patients with MCAD deficiency. This mutation is responsible for about 90% of mutant MCAD alleles in Caucasians. Patients with this type of mutation have a variety of symptoms, indicating that the clinical heterogeneity of MCAD deficiency may not be caused entirely by genetic heterogeneity. Screening for the mutation among newborns in England, Australia, and United States of America indicates the prevalence of carriers to be 1 in 40-107, suggesting the high incidence of the mutation. Since presymptomatic diagnosis and appropriate dietary management are important in MCAD deficiency to prevent life-threatening complications, the relatively high incidence of this disorder may warrant population screening. The most common MCAD mutation can now be detected by DNA diagnostic methods using Guthrie cards. This makes it possible to screen a population efficiently for this potentially fatal disorder.
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Affiliation(s)
- Y Matsubara
- Department of Biochemical Genetics, Tohoku University School of Medicine, Sendai, Japan
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Goradia TM, Stanton VP, Cui XF, Aburatani H, Li HH, Lange K, Housman DE, Arnheim N. Ordering three DNA polymorphisms on human chromosome 3 by sperm typing. Genomics 1991; 10:748-55. [PMID: 1679751 DOI: 10.1016/0888-7543(91)90459-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Three loci on the short arm of human chromosome 3 were ordered by sperm typing to expand the limited genetic map of this region. Almost 300 individual sperm from a donor triply heterozygous at D3S2, D3S11, and D3S12 were amplified by PCR using primers flanking the polymorphic site at each locus. Primary PCR product was reamplified using allele-specific primers of different lengths, allowing the allelic state at each locus to be determined by gel electrophoresis. Maximum likelihood analysis of the sperm-typing data showed that the most likely order was D3S2-D3S11-D3S12 with an odds ratio of almost 5000:1 when compared to the next most likely order. This finding should be useful in interpreting loss of heterozygosity on 3p in a variety of cancers. Our results also demonstrate the practicality of ordering DNA polymorphisms using sperm typing.
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Affiliation(s)
- T M Goradia
- Department of Biomathematics, University of California, Los Angeles 90032
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Affiliation(s)
- M Super
- Royal Manchester Children's Hospital, Pendlebury, UK
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