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Shan J, Wu T, Wei W, Huang J, Li Y, Zou B, Ma Y, Cui L, Wu H, Zhou G. Visualized RNA detection of SARS-CoV-2 in a closed tube by coupling RT-PCR with nested invasive reaction. Analyst 2023; 148:995-1004. [PMID: 36723063 DOI: 10.1039/d2an01679f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A simple, cost-effective and reliable diagnosis of pathogen nucleic acids assay is much required for controlling a pandemic of a virus disease, such as COVID-19. Our previously developed visualized detection of pathogen DNA in a single closed tube is very suitable for POCT. However, virus RNA could not be detected directly and should be reverse-transcribed into cDNA in advance. To enable this visualized assay to detect virus RNA directly, various types of reverse transcriptase were investigated, and finally we found that HiScript II reverse transcriptase could keep active and be well adapted to the one-pot visualized assay in optimized conditions. Reverse transcription, template amplification and amplicon identification by PCR coupled with invasive reaction, as well as visualization by self-assembling of AuNP probes could be automatically and sequentially performed in a closed tube under different temperature conditions, achieving "sample (RNA)-in-result (red color)-out" only by a simple PCR engine plus the naked eye. The visualized RT-PCR is sensitive to unambiguous detection of 5 copies of the N and ORFlab genes of SARS-CoV-2 RNA comparing favourably with qPCR methods (commercialized kit), is specific to genotype 3 variants (Alpha, Beta and Omicron) of SARS-CoV-2, and is very accurate for picking up 0.01% Omicron variant from a large amount of sequence-similar backgrounds. The method is employed in detecting 50 clinical samples, and 10 of them were detected as SARS-CoV-2 positive samples, identical to those by conventional RT-PCR, indicating that the method is cost-effective and labor-saving for pathogen RNA screening in resource-limited regions.
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Affiliation(s)
- Jingwen Shan
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Tao Wu
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China.
| | - Wei Wei
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Jinling Huang
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Yijun Li
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China. .,School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Yi Ma
- State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210023, China
| | - Lunbiao Cui
- NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China.
| | - Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China. .,School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China. .,School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210023, China.,School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
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Ren L, Ming Z, Zhang W, Liao Y, Tang X, Yan B, Lv H, Xiao X. Shared-probe system: An accurate, low-cost and general enzyme-assisted DNA probe system for detection of genetic mutation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Sharafdarkolaee SH, Gill P, Motovali-Bashi M, Sharafdarkolaee FH. Isothermal Amplification Methods for the SNP Genotyping. Curr Mol Med 2019; 19:461-472. [PMID: 31131752 DOI: 10.2174/1566524019666190527083947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 06/30/2018] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
Abstract
The demands for genotyping techniques with acceptable precision, accuracy, cost-effectiveness in high throughput formats made driving forces for continuous development of novel technologies. A wide range of mutation detection techniques based on polymerase chain reaction (PCR) have been introduced. The best alternatives were the isothermal amplification technologies that those did not require a thermal cycler. In this review, we aimed to describe the most known isothermal amplification techniques for SNP genotyping.
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Affiliation(s)
| | - Pooria Gill
- Nanomedicine Group, Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Motovali-Bashi
- Department of Genetics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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Erdem A, Eksin E. Magnetic beads assay based on Zip nucleic acid for electrochemical detection of Factor V Leiden mutation. Int J Biol Macromol 2018; 125:839-846. [PMID: 30552928 DOI: 10.1016/j.ijbiomac.2018.12.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 01/11/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation among people. Development of reliable methods for the detection of SNP is crucial in aspects of molecular diagnosis and personalized medicine. In our study, a genomagnetic assay in combination with zip nucleic acid (ZNA) for electrochemical detection of SNP related to Factor V Leiden mutation. For the first time in the literature, a new generation nucleic acid; ZNA was applied herein for electrochemical monitoring of nucleic acid hybridization. Streptavidin coated magnetic beads (MBs) were used for preparation of samples containing ZNA-DNA hybrid and accordingly, the guanine signal was measured as a response of hybridization related to Factor V Leiden mutation by carbon nanofibers (CNF) modified screen printed electrodes (SPE) and multi-channel screen printed array of electrodes (CNF-MULTI SPEx8). The detection limit (DL) was found to be 3.79 μg/mL (376 nM) and, 11.63 μg/mL (1.624 μM), respectively by CNF-SPE and CNF-MULTI SPEx8. The selectivity of ZNA probe to mutation-free DNA sequences was also investigated in contrast to DNA probe. The applicability of ZNA based magnetic beads assay to sequence selective hybridization related to Factor V Leiden was also tested in synthetic PCR samples.
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Affiliation(s)
- Arzum Erdem
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir 35100, Turkey; Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir 35100, Turkey.
| | - Ece Eksin
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir 35100, Turkey; Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir 35100, Turkey
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Heidari Sharafdarkolaee S, Motovali-Bashi M, Gill P. The sensitive detection of IVSII-1(G˃A) mutation in beta globin gene using a Nano-based ligation genotyping system. Gene 2018; 674:98-103. [PMID: 29913238 DOI: 10.1016/j.gene.2018.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 06/02/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
Beta-thalassemia (β-thalassemia) is a globally genetic diseases, and is most prevalent in the Middle East, particularly in Iran. Carrier detection and prenatal diagnosis are the best ways to managing it, and to prevent new community cases from emerging. We report on a simple method for rapid detection of the worst β-thalassemia point mutation in Iran (IVS-II-1 G>A), using a nano-based ligation assay, this was performed using probes with labeled magnetic nanoparticles and quantum dots. After optimizing the technique, 50 DNA samples were genotyped with this method. We found a frequency of 72% for IVSII-1 (G˃A) mutation (42% heterozygote, and 30% mutant homozygote) with a highly sensitive nano-based ligation genotyping system, offering excellent sensitivity and specificity for point mutation detection; it has been demonstrated to be inaccurate, sensitive, cost-effective, and rapid technique for single nucleotide polymorphism (SNP) genotyping.
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Affiliation(s)
| | - Majid Motovali-Bashi
- Genetics Division, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
| | - Pooria Gill
- Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran; Nanomedicine Group, Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
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Nejman-Faleńczyk B, Bloch S, Januszkiewicz A, Węgrzyn A, Węgrzyn G. A simple and rapid procedure for the detection of genes encoding Shiga toxins and other specific DNA sequences. Toxins (Basel) 2015; 7:4745-57. [PMID: 26580652 PMCID: PMC4663531 DOI: 10.3390/toxins7114745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/26/2015] [Accepted: 11/10/2015] [Indexed: 11/25/2022] Open
Abstract
A novel procedure for the detection of specific DNA sequences has been developed. This procedure is based on the already known method employing PCR with appropriate primers and a sequence-specific DNA probe labeled with the fluorescent agent 6-carboxylfluorescein (FAM) at the 5′ end and the fluorescence quencher BHQ-1 (black hole quencher) at the 3′ end. However, instead of the detection of the fluorescence signal with the use of real-time PCR cyclers, fluorescence/luminescence spectrometers or fluorescence polarization readers, as in all previously-reported procedures, we propose visual observation of the fluorescence under UV light directly in the reaction tube. An example for the specific detection of the Shiga toxin-producing Escherichia coli (STEC) strains, by detecting Shiga toxin genes, is demonstrated. This method appears to be specific, simple, rapid and cost effective. It may be suitable for use in research laboratories, as well as in diagnostic units of medical institutions, even those equipped only with a thermocycler and a UV transilluminator, particularly if rapid identification of a pathogen is required.
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Affiliation(s)
- Bożena Nejman-Faleńczyk
- Depratment of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Sylwia Bloch
- Depratment of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Aleksandra Januszkiewicz
- Department of Bacteriology, National Institute of Public Health-Public Institute of Hygiene, 24 Chocimska Street, 00-791 Warsaw, Poland.
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology (affiliated with the University of Gdansk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Grzegorz Węgrzyn
- Depratment of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
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7
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Li S, Wang Z, Zhou L, Luo F, Zhao C. Fluorescence polarization-based method with bisulfite conversion-specific one-label extension for quantification of single CpG dinucleotide methylation. Genome 2015; 58:357-63. [DOI: 10.1139/gen-2014-0185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To quantify the methylation at individual CpG dinucleotide sites in large biological or clinical samples, we developed a bisulfite conversion-specific one-label extension (BS-OLE) method using visualization by fluorescence polarization (FP) measurement of methylation at single CpG sites in small amounts of genomic DNA. Genomic DNA was treated with sodium bisulfite to convert unmethylated cytosine to uracil leaving 5-methylcytosine unaltered, and BS-PCR was used to generate DNA template containing target CpG sites. BS-OLE uses a BS-primer hybridized immediately upstream of the target CpG site being examined and then fluorescent dCTP or dUTP is incorporated into the methylated (CpG) or unmethylated (TpG) form of the target site through single-nucleotide chain extension, yielding an FP ratio between the fluorescent dCTP- and dUTP-incorporated products as a measure of methylation. This provides stable estimates of the methylation level of human genomic DNA and of a 250-bp plasmid DNA segment containing a single TCGA TaqI cleavage site, in accordance with the results of a combined bisulfite restriction analysis method. We used BS-OLE to measure dose-dependent DNA hypomethylation in human embryonic kidney 293T cells treated with the DNA methyltransferase inhibitor 5-aza-dC. BS-OLE is well suited to high-throughput multi-sample applications in biological and medical studies.
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Affiliation(s)
- Shufen Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
| | - Zhongju Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
| | - Lin Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
| | - Fu Luo
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, No. 1023 Shatai Road, Baiyun District, Guangzhou City, Guangdong Province 510515, China
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Wang J, Zou B, Rui J, Song Q, Kajiyama T, Kambara H, Zhou G. Exponential amplification of DNA with very low background using graphene oxide and single-stranded binding protein to suppress non-specific amplification. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1426-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Zhao C, Xue H. A simple method for high-throughput quantification of genome-wide DNA methylation by fluorescence polarization. Epigenetics 2014; 7:335-9. [DOI: 10.4161/epi.19376] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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10
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Analysis of single nucleotide polymorphism in human angiogenin using droplet-based microfluidics. BIOCHIP JOURNAL 2014. [DOI: 10.1007/s13206-014-8103-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Tambouret R. Female genital tract. Cancer Treat Res 2014; 160:241-272. [PMID: 24092373 DOI: 10.1007/978-3-642-38850-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Rosemary Tambouret
- Department of Pathology, Massachusetts General Hospital, Warren 105/55 Fruit Street, Boston, MA, 02114, USA,
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12
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Tang L, Chun IS, Wang Z, Li J, Li X, Lu Y. DNA detection using plasmonic enhanced near-infrared photoluminescence of gallium arsenide. Anal Chem 2013; 85:9522-7. [PMID: 24079346 DOI: 10.1021/ac401169c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Efficient near-infrared detection of specific DNA with single nucleotide polymorphism selectivity is important for diagnostics and biomedical research. Herein, we report the use of gallium arsenide (GaAs) as a sensing platform for probing DNA immobilization and targeting DNA hybridization, resulting in ∼8-fold enhanced GaAs photoluminescence (PL) at ∼875 nm. The new signal amplification strategy, further coupled with the plasmonic effect of Au nanoparticles, is capable of detecting DNA molecules with a detection limit of 0.8 pM and selectivity against single base mismatches. Such an ultrasensitive near-infrared sensor can find a wide range of biochemical and biomedical applications.
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Affiliation(s)
- Longhua Tang
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University , Beijing, China 100084
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Joshi PH, Xu H, LeStrange R, Flockhart N, Kirkland B, Vazquez G, Qian Z, Sharma A, Marvasty I, Bhatt K, Brown C, Rinehart S, Miller J, Voros S. The M235T single nucleotide polymorphism in the angiotensinogen gene is associated with coronary artery calcium in patients with a family history of coronary artery disease. Atherosclerosis 2013; 226:433-9. [DOI: 10.1016/j.atherosclerosis.2012.10.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 09/21/2012] [Accepted: 10/09/2012] [Indexed: 11/17/2022]
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Yu Y, Liu Y, Zhen SJ, Huang CZ. A graphene oxide enhanced fluorescence anisotropy strategy for DNAzyme-based assay of metal ions. Chem Commun (Camb) 2013; 49:1942-4. [DOI: 10.1039/c3cc38129c] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Eto M, Kamba T, Miyake H, Fujisawa M, Kamai T, Uemura H, Tsukamoto T, Azuma H, Matsubara A, Nishimura K, Nakamura T, Ogawa O, Naito S. STAT3 polymorphism can predict the response to interferon-α therapy in patients with metastatic renal cell carcinoma. Eur Urol 2012; 63:745-52. [PMID: 23063454 DOI: 10.1016/j.eururo.2012.09.052] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/19/2012] [Indexed: 02/02/2023]
Abstract
BACKGROUND In our 2007 retrospective study, we reported that single nucleotide polymorphisms (SNPs) in the signal transducer and activator of transcription 3 (acute-phase response factor) (STAT3) gene were significantly associated with better response to interferon (IFN)-α in patients with metastatic renal cell carcinoma (mRCC). OBJECTIVE To prospectively confirm those results, the Japan Immunotherapy SNPs-Study Group for Kidney Cancer conducted this trial. DESIGN, SETTING, AND PARTICIPANTS In this multicenter, prospective study, 203 eligible patients were enrolled. We evaluated the correlation between the antitumor effects of IFN-α and 11 SNPs (STAT3-2, STAT3-0, SOCS3-1, IL4R-34, PTGS1-3, PTGS1-4, PTGS1-5, PTGS2-12, IRF2-67, ICSBP-38, and TAP2-5) in eight genes in 180 patients who received IFN-α for >12 wk. INTERVENTIONS Patients were treated with three doses per week of IFN-α 5 million IU. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We analyzed the association of response to IFN-α and overall survival (OS) with genetic polymorphisms using a chi-square test and a logistic regression model. RESULTS AND LIMITATIONS The response rate of IFN-α was 13.8% (28 of 203 patients; 9 complete responses [CRs], 19 partial responses [PRs]). The CR rate of 4.4% was higher than we expected. Response to IFN-α was not associated with any of the 11 SNPs examined. However, when we assessed patients with CR, PR, and stable disease >24 wk as a group representing those with clinical response, a significant association was observed between STAT3-2 (rs1905341) and the clinical response of IFN-α (p=0.039). Namely, C/C genotype of STAT3-2 was significantly associated with the clinical response of IFN-α and OS. These results were generated in Japanese patients and should be studied in other ethnic groups. CONCLUSIONS This is the first prospective study demonstrating that a STAT3 polymorphism can be a predictive marker for treatment with IFN-α for patients with mRCC.
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Affiliation(s)
- Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Li-Na Pu, Ze Zhao, Yuan-Ting Zhang. Investigation on Cardiovascular Risk Prediction Using Genetic Information. ACTA ACUST UNITED AC 2012; 16:795-808. [DOI: 10.1109/titb.2012.2205009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Ahmed MU, Dunn L, Ivanova EP. Evaluation of Current Molecular Approaches for Genotyping ofCampylobacter jejuniStrains. Foodborne Pathog Dis 2012; 9:375-85. [DOI: 10.1089/fpd.2011.0988] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Monir U. Ahmed
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
| | - Louise Dunn
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
| | - Elena P. Ivanova
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
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Sugita N, Kobayashi T, Kikuchi A, Shimada Y, Hirano E, Sasahara J, Tanaka K, Yoshie H. Immunoregulatory gene polymorphisms in Japanese women with preterm births and periodontitis. J Reprod Immunol 2012; 93:94-101. [PMID: 22382006 DOI: 10.1016/j.jri.2012.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 12/13/2011] [Accepted: 01/27/2012] [Indexed: 11/18/2022]
Abstract
Many studies have reported an association between periodontal disease and preterm birth, although this remains controversial. Cytokines and antibodies produced to give resistance to infection can enter the bloodstream and cause preterm labor. We analyzed maternal genetic polymorphisms in various immunoregulatory genes that could affect both preterm birth and periodontitis. A total of 1099 women referred to the Department of Obstetrics and Gynecology, Niigata University Medical and Dental Hospital were candidates for participation, 424 of whom refused, and 553 were excluded. The final number of subjects was 122 (51 with preterm birth, 71 with term birth). Genomic DNA was isolated from venous blood, and 22 polymorphisms were determined: IL-1A, IL-1B, IL-1RN, IL-2, IL-4, IL-6, IL-10, TNFA, TNFRI, TNFRII, FcγRIIA, FcγRIIB, FcγRIIIA, FcγRIIIB, and FcαR. Within five days of labor, periodontal parameters were evaluated, and bacteria from subgingival plaque were detected using real-time PCR. There was no difference in the prevalence and degree of periodontitis between term and preterm births. Chi-squared tests showed that an age <33 years and FcαR(+56)T/C alleles were associated with preterm birth. Multiple logistic regression analysis represented a model with significant fitness in which four variables were associated with preterm birth: maternal age, number of Aggregatibacter actinomycetemcomitans, IL-6(-572)G/C, and FcαR(+56)T/C. In conclusion, there was no association between preterm birth and periodontitis in this study. A. actinomycetemcomitans, IL-6, and FcαR were suggested to be associated with preterm birth. Multiple logistic regression models with both genetic and environmental factors would be useful for evaluating susceptibility to preterm birth.
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Affiliation(s)
- Noriko Sugita
- Division of Periodontology, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
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Oh H, Smith CL. Evolving methods for single nucleotide polymorphism detection: Factor V Leiden mutation detection. J Clin Lab Anal 2012; 25:259-88. [PMID: 21786330 DOI: 10.1002/jcla.20470] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The many techniques used to diagnose the Factor V Leiden (FVL) mutation, the most common hereditary hypercoagulation disorder in Eurasians, and the most frequently requested genetic test reflect the evolving strategies in protein and DNA diagnosis. METHODS Here, molecular methods to diagnose the FVL mutation are discussed. RESULTS Protein-based detection assays include the conventional functional activated protein C resistance coagulation test and the recently reported antibody-mediated sensor detection; and DNA-based assays include approaches that use electrophoretic fractionation e.g., restriction fragment length polymorphism, denaturing gradient gel electrophoresis, and single-stranded conformational PCR analysis, DNA hybridization (e.g., microarrays), DNA polymerase-based assays, e.g., extension reactions, fluorescence polarization template-directed dye-terminator incorporation, PCR assays (e.g., amplification-refractory mutation system, melting curve analysis using real-time quantitative PCR, and helicase-dependent amplification), DNA sequencing (e.g., direct sequencing, pyrosequencing), cleavase-based Invader assay and ligase-based assays (e.g., oligonucleotide ligation assay and ligase-mediated rolling circle amplification). CONCLUSION The method chosen by a laboratory to diagnose FVL not only depends on the available technical expertise and equipment, but also the type, variety, and extent of other genetic disorders being diagnosed.
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Affiliation(s)
- Herin Oh
- Molecular Biotechnology Research Laboratory, Boston University, Boston, MA, USA.
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20
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Integration of rolling circle amplification and cationic conjugated polymer for the homogeneous detection of single nucleotide polymorphisms. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4663-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Pan X, Ju J, Zhan Y, Wu D. Preparation and Fluorescence Characteristics of Amido-Functionalized Dual-Fluorescent Microspheres with Core/Shell Structure. MACROMOL CHEM PHYS 2010. [DOI: 10.1002/macp.201000243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Chien MP, Thompson MP, Gianneschi NC. DNA-nanoparticle micelles as supramolecular fluorogenic substrates enabling catalytic signal amplification and detection by DNAzyme probes. Chem Commun (Camb) 2010; 47:167-9. [PMID: 20830351 DOI: 10.1039/c0cc02291h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic DNA molecules have tremendous potential in propagating detection events via nucleic acid sequence selective signal amplification. However, they suffer from product inhibition limiting their widespread utility. Herein, this limitation is overcome utilizing a novel fluorogenic substrate design consisting of cooperatively assembled DNA-nanoparticle micelles.
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Affiliation(s)
- Miao-Ping Chien
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Jenkins S, Gibson N. High-throughput SNP genotyping. Comp Funct Genomics 2010; 3:57-66. [PMID: 18628885 PMCID: PMC2447245 DOI: 10.1002/cfg.130] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2001] [Accepted: 11/19/2001] [Indexed: 12/24/2022] Open
Abstract
Whole genome approaches using single nucleotide polymorphism (SNP) markers have the
potential to transform complex disease genetics and expedite pharmacogenetics research.
This has led to a requirement for high-throughput SNP genotyping platforms.
Development of a successful high-throughput genotyping platform depends on coupling
reliable assay chemistry with an appropriate detection system to maximise efficiency with
respect to accuracy, speed and cost. Current technology platforms are able to deliver
throughputs in excess of 100 000 genotypes per day, with an accuracy of >99%, at a cost
of 20–30 cents per genotype. In order to meet the demands of the coming years, however,
genotyping platforms need to deliver throughputs in the order of one million genotypes per
day at a cost of only a few cents per genotype. In addition, DNA template requirements
must be minimised such that hundreds of thousands of SNPs can be interrogated using a
relatively small amount of genomic DNA. As such, it is predicted that the next generation
of high-throughput genotyping platforms will exploit large-scale multiplex reactions and
solid phase assay detection systems.
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Affiliation(s)
- Suzanne Jenkins
- R&D Genetics, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.
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Abstract
Genetic variants at multiple loci have been shown to be associated with susceptibility to periodontitis. To better assess the genetic risk factors for periodontitis, we performed a case-control study in 319 Japanese individuals with periodontitis (172 aggressive and 147 chronic disease) and 303 race-matched healthy control individuals. Thirty-five functional gene polymorphisms that had been previously associated with immune responses were genotyped. For all gene polymorphisms tested, no significant differences were observed in the allele frequencies of persons with aggressive, chronic, and combined (aggressive and chronic) periodontitis, compared with control individuals. Multiple logistic regression analysis revealed a significant association of the vitamin D receptor +1056 T/C polymorphism with susceptibility to chronic periodontitis, after adjustment for age, gender, and smoking status (P = 0.002). These results suggest that none of the polymorphisms tested was strongly associated with periodontitis in a Japanese population. However, the vitamin D receptor +1056 polymorphism may be related to chronic periodontitis.
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Fujita H, Kobayashi T, Tai H, Nagata M, Hoshina H, Nishizawa R, Takagi R, Yoshie H. Assessment of 14 functional gene polymorphisms in Japanese patients with oral lichen planus: a pilot case-control study. Int J Oral Maxillofac Surg 2009; 38:978-83. [DOI: 10.1016/j.ijom.2009.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/20/2008] [Accepted: 05/05/2009] [Indexed: 01/12/2023]
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Kobayashi T, Murasawa A, Ito S, Yamamoto K, Komatsu Y, Abe A, Sumida T, Yoshie H. Cytokine gene polymorphisms associated with rheumatoid arthritis and periodontitis in Japanese adults. J Periodontol 2009; 80:792-9. [PMID: 19405833 DOI: 10.1902/jop.2009.080573] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Cytokines play a major role in the pathogenesis of rheumatoid arthritis (RA) and periodontitis. Both diseases were previously shown to be partly influenced by cytokine gene polymorphisms. Therefore, we evaluated whether the distributions of the cytokine genotypes were unique to subjects with both diseases. METHODS The study subjects consisted of Japanese adults with RA (RA group; n = 153), periodontitis only (P group; n = 117), and healthy individuals (H group; n = 108). Clinical periodontal condition was defined by measurements of probing depth, clinical attachment level, and bleeding on probing. Genomic DNA was isolated from peripheral blood and analyzed for the determination of 16 gene polymorphisms encoding interleukin (IL)-1, -2, -4, -6, and -10, tumor necrosis factor-alpha, and transforming growth factor-beta 1. RESULTS The frequency of patients with RA who exhibited periodontitis was 89.5% (RA + P group; n = 137). No significant differences were observed in any of the frequencies of cytokine genotypes and alleles among the subject groups. After adjustment for age, gender, and smoking status, multiple logistic regression analysis revealed a significant difference in the distribution of IL-1B +3954 genotypes between RA + P and P groups (P = 0.006) and between RA + P and H groups (P = 0.008). CONCLUSION Japanese individuals with RA and periodontitis may exhibit different distributions of IL-1B +3954 genotypes than healthy controls and subjects with periodontitis only.
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Affiliation(s)
- Tetsuo Kobayashi
- General Dentistry and Clinical Education Unit, Niigata University Medical and Dental Hospital, Niigata, Japan.
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Nakahara H, Sekiguchi K, Hosono N, Kubo M, Takahashi A, Nakamura Y, Kasai K. Criterion values for multiplex SNP genotyping by the invader assay. Forensic Sci Int Genet 2009; 4:130-6. [PMID: 20129472 DOI: 10.1016/j.fsigen.2009.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 07/03/2009] [Accepted: 07/22/2009] [Indexed: 10/20/2022]
Abstract
We have developed a multiplex, single nucleotide polymorphism (SNP) typing system for forensic identification, based on the Invader assay. Using this system, fluorescence data for 21 SNP loci were collected and analyzed. We used endpoint genotyping, commonly used with the Invader assay, and also developed more reliable typing criteria because endpoint typing was occasionally unable to clearly identify the genotype of some loci. Analysis of the fluorescence data identified criteria that had high reproducibility for each genotype. One such criterion is the climbing angle of the curve resulting from two-dimensional plots of the two kinds of fluorescence used for the Invader assay. The climbing angle was observed at the time during the reaction when either or both of the fluorescence intensities increased most significantly. The angles were remarkably associated with homozygous genotypes. On the other hand, all heterozygote endpoint fluorescence ratios were highly reproducible and had very little aberration. These values enabled SNP typing to be more clearly defined compared with typing using only the endpoint fluorescence ratio, which is commonly used with the Invader assay. The values suggested in this study are easily calculated from raw fluorescence data and will be useful for multiplex SNP typing based on the Invader assay.
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Affiliation(s)
- Hiroaki Nakahara
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
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Atsumi H, Yoshimoto K, Saito S, Ohkuma M, Maeda M, Nagasaki Y. Luminescence-based colorimetric discrimination of single-nucleotide transversions by the combined use of the derivatives of DOTA-conjugated naphthyridine and its terbium complex. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.02.152] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Furukawa K, Abe H, Wang J, Uda M, Koshino H, Tsuneda S, Ito Y. Reduction-triggered red fluorescent probes for dual-color detection of oligonucleotide sequences. Org Biomol Chem 2008; 7:671-7. [PMID: 19194582 DOI: 10.1039/b817228e] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a new red fluorogenic compound derived from naphthorhodamine for a reduction-triggered fluorescence probe to sense oligonucleotides. The fluorogenic reaction between naphthorhodamine azide derivatives and reducing reagents such as triphenylphosphine (TPP) on the DNA target does not use any enzyme or reagent, and fluoresces at 650 nm. The probes were used for dual color detection of a single nucleotide difference on the leukemia-related bcr/abl gene.
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Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, Advance Science Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama 351-0198, Japan
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Duffy KJ, Littrell J, Locke A, Sherman SL, Olivier M. A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay. Nucleic Acids Res 2008; 36:e145. [PMID: 18940863 PMCID: PMC2602776 DOI: 10.1093/nar/gkn736] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Individuals with trisomy 21 display complex phenotypes with differing degrees of severity. Numerous reliable methods have been established to diagnose the initial trisomy in these patients, but the identification and characterization of the genetic basis of the phenotypic variation in individuals with trisomy remains challenging. To date, methods that can accurately determine genotypes in trisomic DNA samples are expensive, require specialized equipment and complicated analyses. Here we report proof-of-concept results for an Invader® assay-based genotyping procedure that can determine SNP genotypes in trisomic genomic DNA samples in a simple and cost-effective manner. The procedure requires only two experimental steps: a real-time measurement of the fluorescent Invader® signal and analysis with a specifically designed clustering algorithm. The approach was tested using genomic DNA samples from 23 individuals with trisomy 21, and results were compared to genotypes previously determined with pyrosequencing. Additional assays for 15 SNPs were tested in a set of 21 DNA samples to assess assay performance. Our method successfully identified the correct SNP genotypes for the trisomic genomic DNA samples tested, and thus provides an alternative to determine SNP genotypes in trisomic DNA samples for subsequent association studies in patients with Down syndrome and other trisomies.
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Affiliation(s)
- Kelly J Duffy
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
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Kwok PY. High-throughput genotyping with primer extension fluorescent polarization detection. ACTA ACUST UNITED AC 2008; Chapter 2:Unit 2.11. [PMID: 18428360 DOI: 10.1002/0471142905.hg0211s39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The primer extension assay with fluorescence polarization (FP) detection is a versatile assay for single nucleotide polymorphism (SNP) genotyping. With proper design, this homogeneous assay works under universal conditions. Fluorescence polarization occurs when a fluorescent dye is excited by plane-polarized light and is detected if the fluorescent dye is part of a large molecule. In assays where small fluorescent molecules are turned into large fluorescent products, FP provides a simple way to determine if the reaction has occurred without the need for separation or purification of the reaction mixture. In the primer extension assay, DNA polymerase incorporates the complementary, allelic nucleotide onto the SNP primer designed to anneal to the target DNA one base upstream of the polymorphic site. When a fluorescently labeled nucleotide is incorporated, high FP is observed for that dye and the genotype of the DNA sample is determined.
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Affiliation(s)
- Pui-Yan Kwok
- University of California, San Francisco, California, USA
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Morinaga K, Yamauchi T, Kimura S, Maekawa T, Ueda T. Overcoming imatinib resistance using Src inhibitor CGP76030, Abl inhibitor nilotinib and Abl/Lyn inhibitor INNO-406 in newly established K562 variants withBCR-ABLgene amplification. Int J Cancer 2008; 122:2621-7. [DOI: 10.1002/ijc.23435] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Joshi VA, Mancini-DiNardo D, Funke BH. Selection of a platform for mutation detection. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.15. [PMID: 18428425 DOI: 10.1002/0471142905.hg0715s56] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
New mutation detection technologies must keep pace by becoming more cost-effective while offering improved technical sensitivity and higher throughput capacity. In recent years, the number of mutation detection platforms available to the clinical researcher has grown to a point where it is difficult to keep track of all available options as well as their benefits and pitfalls. This unit provides an entry point for a variety of researchers who wish to analyze samples for known or novel mutations and need to determine which platform is most suited for their particular needs. A practical guide is provided in this unit, including a brief overview, information on assay parameters, design and cost considerations, as well as platform flexibility and scalability of the assay. Although the focus here is on applications involving human disease, many of these platforms can be easily adapted to the study of other organisms.
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Affiliation(s)
- Victoria A Joshi
- Harvard Medical School-Partners Healthcare Center for Genetics and Genomics, Cambridge, Massachusetts, USA
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Ito N, Eto M, Nakamura E, Takahashi A, Tsukamoto T, Toma H, Nakazawa H, Hirao Y, Uemura H, Kagawa S, Kanayama H, Nose Y, Kinukawa N, Nakamura T, Jinnai N, Seki T, Takamatsu M, Masui Y, Naito S, Ogawa O. STAT3Polymorphism Predicts Interferon-Alfa Response in Patients With Metastatic Renal Cell Carcinoma. J Clin Oncol 2007; 25:2785-91. [PMID: 17602083 DOI: 10.1200/jco.2006.09.8897] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
PurposeTo clarify the effect of genetic polymorphisms on the response to interferon alfa (IFN-α) for metastatic renal cell carcinoma (MRCC), and to find a reliable molecular marker to select those patients with MRCC who would benefit from IFN-α immunotherapy.Patients and MethodsWe carried out an association study in which 463 single nucleotide polymorphisms (SNPs) in 33 candidate genes were genotyped in 75 Japanese patients who had received IFN-α for MRCC.ResultsAfter adjusting for lung metastasis, stepwise logistic regression analysis revealed that the SNPs in signal transducer and activator 3 (STAT3) were most significantly associated with better response to IFN-α. Linkage disequilibrium mapping revealed that the SNP in the 5′ region of STAT3, rs4796793, was the most significant predictor of IFN-α response (odds ratio [OR] = 2.73; 95% CI, 1.38 to 5.78). The highest OR was shown in the CC genotype at rs4796793 compared to the GG + GC genotypes (OR = 8.38, 95% CI, 1.63 to 42.96). Genotype-dependent expressions of STAT3 in B lymphocyte cell lines and the enhanced growth inhibitory effects of IFN-α by STAT3 suppression in an RCC cell line supported the results of the present association study.ConclusionThe present study suggested that the STAT3 polymorphism is a useful diagnostic marker to predict the response to IFN-α therapy in patients with MRCC. An efficient response marker for IFN-α needs to be utilized to establish individual optimal treatment strategies, even when newer drug therapies are used as first line treatments for MRCC.
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Affiliation(s)
- Noriyuki Ito
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Grundberg E, Akesson K, Kindmark A, Gerdhem P, Holmberg A, Mellström D, Ljunggren O, Orwoll E, Mallmin H, Ohlsson C, Brändström H. The impact of estradiol on bone mineral density is modulated by the specific estrogen receptor-alpha cofactor retinoblastoma-interacting zinc finger protein-1 insertion/deletion polymorphism. J Clin Endocrinol Metab 2007; 92:2300-6. [PMID: 17356055 DOI: 10.1210/jc.2006-1572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Estrogens regulate bone mass by binding to the estrogen receptor (ER)-alpha as well as ER-beta. The specific ERalpha cofactor retinoblastoma-interacting zinc finger protein (RIZ)-1 enhances ERalpha function in the presence of estrogen. OBJECTIVE The objective of the study was to determine whether a RIZ P704 insertion (+)/deletion (-) (indel) polymorphism modulates the impact of estradiol on bone mineral density (BMD) and study the association between the polymorphism and BMD in elderly subjects. DESIGN This was a population-based, prospective, and cross-sectional study, the Swedish MrOS Study, and the Malmö OPRA Study, respectively. SETTING The study was conducted at three academic medical centers: Sahlgrenska Academy in Gothenburg, Malmö University Hospital, and Uppsala University Hospital. PARTICIPANTS In total, 4058 men and women, aged 69-81 yr, were randomly selected from population registries. MAIN OUTCOME MEASURES BMD (grams per square centimeter) was measured at femoral neck, trochanter, lumbar spine, and total body. RESULTS The RIZ P704(+/+) genotype was associated with low BMD in both women (femoral neck, P < 0.001; trochanter, P < 0.01; lumbar spine, P < 0.05; total body, P < 0.01) and men (lumbar spine, P < 0.05). However, the association between the polymorphism and BMD was dependent on estradiol status. The positive correlation between serum estradiol and BMD was significantly modulated by the genotype with a stronger correlation in the P704(+/+) group than the P704(-/-) group (r = 0.19 vs. r = 0.08, P < 0.05). CONCLUSIONS These large-scale studies of elderly men and women indicate that the ERalpha cofactor RIZ gene has a prominent effect on BMD, and the P704 genotype modulates the impact of estradiol on BMD. Further studies are required to determine whether this polymorphism modulates the estrogenic response to estradiol treatment.
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Affiliation(s)
- Elin Grundberg
- Department of Medical Sciences, Uppsala University Hospital, Ing 70, 3 tr, Uppsala, Sweden.
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Ahmed MU, Idegami K, Chikae M, Kerman K, Chaumpluk P, Yamamura S, Tamiya E. Electrochemical DNA biosensor using a disposable electrochemical printed (DEP) chip for the detection of SNPs from unpurified PCR amplicons. Analyst 2007; 132:431-8. [PMID: 17471389 DOI: 10.1039/b615242b] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we are reporting for the first time the elucidation of single nucleotide polymorphisms (SNPs) of clinically important alleles from consenting human subjects using a disposable electrochemical printed (DEP) chip in connection with differential pulse voltammetry (DPV) and a redox active molecule Hoechst 33258 [H33258, 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi(1H-benzimidazole)]. Post-PCR products were analyzed directly without any purification process. The aggregation of the DNA-H33258 complex causes a significant drop in the peak current intensity of H33258 oxidation. The phenomenon of DNA aggregation induced by H33258 in addition to changes in anodic current peak are used to detect SNPs. Since laborious probe immobilization was not required, our biosensor offers several benefits due to its simplicity and rapid response as a promising device for genetic analysis.
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Affiliation(s)
- Minhaz Uddin Ahmed
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa 923-1292, Japan
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Kutyavin IV, Milesi D, Belousov Y, Podyminogin M, Vorobiev A, Gorn V, Lukhtanov EA, Vermeulen NMJ, Mahoney W. A novel endonuclease IV post-PCR genotyping system. Nucleic Acids Res 2006; 34:e128. [PMID: 17012270 PMCID: PMC1636472 DOI: 10.1093/nar/gkl679] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Revised: 08/29/2006] [Accepted: 09/05/2006] [Indexed: 11/21/2022] Open
Abstract
Here we describe a novel endonuclease IV (Endo IV) based assay utilizing a substrate that mimics the abasic lesions that normally occur in double-stranded DNA. The three component substrate is characterized by single-stranded DNA target, an oligonucleotide probe, separated from a helper oligonucleotide by a one base gap. The oligonucleotide probe contains a non-fluorescent quencher at the 5' end and fluorophore attached to the 3' end through a special rigid linker. Fluorescence of the oligonucleotide probe is efficiently quenched by the interaction of terminal dye and quencher when not hybridized. Upon hybridization of the oligonucleotide probe and helper probe to their complementary target, the phosphodiester linkage between the rigid linker and the 3' end of the probe is efficiently cleaved, generating a fluorescent signal. In this study, the use of the Endo IV assay as a post-PCR amplification detection system is demonstrated. High sensitivity and specificity are illustrated using single nucleotide polymorphism detection.
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Affiliation(s)
| | - Dave Milesi
- Nanogen, 21720 23rd Drive SESuite 150, Bothell, WA 98021, USA
| | | | | | - Alexei Vorobiev
- Nanogen, 21720 23rd Drive SESuite 150, Bothell, WA 98021, USA
| | - Vladimir Gorn
- Nanogen, 21720 23rd Drive SESuite 150, Bothell, WA 98021, USA
| | | | | | - Walt Mahoney
- Nanogen, 21720 23rd Drive SESuite 150, Bothell, WA 98021, USA
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Yu Z, Chen J, Shi H, Stoeber G, Tsang SY, Xue H. Analysis of GABRB2 association with schizophrenia in German population with DNA sequencing and one-label extension method for SNP genotyping. Clin Biochem 2006; 39:210-8. [PMID: 16472798 DOI: 10.1016/j.clinbiochem.2006.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Revised: 11/17/2005] [Accepted: 01/02/2006] [Indexed: 10/25/2022]
Abstract
OBJECTIVES Schizophrenia (SCZ) is a complex mental disease that affects approximately 1% of the population. In this study, six SNPs in GABRB2 were genotyped for a case-control association study with the cycloid psychosis subtype of SCZ in the German population using two methods for SNP genotyping. DESIGN AND METHODS The SNPs were genotyped by direct DNA sequencing, as well as a novel one-label extension method. The results were analyzed for association with SCZ. RESULTS AND CONCLUSIONS Significant association was found for SNPs rs1816071 and rs1816072 with SCZ susceptibility. This is consistent with our previous finding of association of SNPs in GABRB2 with SCZ susceptibility in Han Chinese. There was a total agreement between the genotyping results from one-label extensions and the results of direct DNA sequencing, thus validating the accuracy of the one-label extension method of SNP genotyping.
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Affiliation(s)
- Zhiliang Yu
- Department of Biochemistry and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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Kofiadi IA, Rebrikov DV. Methods for detecting single nucleotide polymorphisms: Allele-specific PCR and hybridization with oligonucleotide probe. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406010029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Poon AH, Laprise C, Lemire M, Hudson TJ, Schurr E. NRAMP1 is not associated with asthma, atopy, and serum immunoglobulin E levels in the French Canadian population. Genes Immun 2005; 6:519-27. [PMID: 15988535 DOI: 10.1038/sj.gene.6364238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reduced infection by mycobacteria, including Mycobacterium tuberculosis, may be partly responsible for increased prevalence of allergic and autoimmune diseases in developed countries. In a murine model of innate resistance to mycobacteria, the Nramp1 gene has been shown to affect asthma susceptibility. From this observation, it was proposed that human NRAMP1 may be a modulator of asthma risk in human populations. To experimentally test the candidacy of NRAMP1 in asthma susceptibility, we characterized five genetic variants of NRAMP1 (5'CAn, 274C>T, 469+14G>C, D543N, and 1729+del4) in an asthma family-based cohort from northeastern Quebec. We did not observe any significant association between NRAMP1 variants (either allele or haplotype specific) with asthma, atopy, or serum immunoglobulin E levels. These results demonstrate that, in spite of direct involvement of Nramp1 in a murine asthma model, in human populations NRAMP1 is not likely to be a major contributor to the genetic etiology of asthma and asthma-related phenotypes.
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Affiliation(s)
- A H Poon
- McGill Centre for the Study of Host Resistance, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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Abstract
The Invader assay uses a structure-specific flap endonuclease (FEN) to cleave a three-dimensional complex formed by hybridization of allele-specific overlapping oligonucleotides to target DNA containing a single nucleotide polymorphism (SNP) site. Annealing of the oligonucleotide complementary to the SNP allele in the target molecule triggers the cleavage of the oligonucleotide by cleavase, a thermostable FEN. Cleavage can be detected by several different approaches. Most commonly, the cleavage product triggers a secondary cleavage reaction on a fluorescence resonance energy transfer (FRET) cassette to release a fluorescent signal. Alternatively, the cleavage can be detected directly by use of fluorescence polarization (FP) probes, or by mass spectrometry. The invasive cleavage reaction is highly specific, has a low failure rate, and can detect zeptomol quantities of target DNA. While the assay traditionally has been used to interrogate one SNP in one sample per reaction, novel chip- or bead-based approaches have been tested to make this efficient and accurate assay adaptable to multiplexing and high-throughput SNP genotyping.
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Affiliation(s)
- Michael Olivier
- Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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Sobrino B, Brión M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 2005; 154:181-94. [PMID: 16182964 DOI: 10.1016/j.forsciint.2004.10.020] [Citation(s) in RCA: 292] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 10/10/2004] [Accepted: 10/15/2004] [Indexed: 11/22/2022]
Abstract
There is an increasing interest in single nucleotide polymorphism (SNP) typing in the forensic field, not only for the usefulness of SNPs for defining Y chromosome or mtDNA haplogroups or for analyzing the geographical origin of samples, but also for the potential applications of autosomal SNPs. The interest of forensic researchers in autosomal SNPs has been attracted due to the potential advantages in paternity testing because of the low mutation rates and specially in the analysis of degraded samples by use of short amplicons. New SNP genotyping methods, chemistries and platforms are continuously being developed and it is often difficult to be keeping up to date and to decide on the best technology options available. This review offers to the reader a state of the art of SNP genotyping technologies with the advantages and disadvantages of the different chemistries and platforms for different forensic requirements.
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Affiliation(s)
- Beatriz Sobrino
- Institute of Legal Medicine, University of Santiago de Compostela, San Francisco s/n, Spain.
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Freeman BD, Buchman TG, Zehnbauer BA. Template-directed dye-terminator incorporation with fluorescence polarization detection for analysis of single nucleotide polymorphisms associated with cardiovascular and thromboembolic disease. Thromb Res 2004; 111:373-9. [PMID: 14698656 DOI: 10.1016/j.thromres.2003.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Bradley D Freeman
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Twist CR, Winson MK, Rowland JJ, Kell DB. Single-nucleotide polymorphism detection using nanomolar nucleotides and single-molecule fluorescence. Anal Biochem 2004; 327:35-44. [PMID: 15033508 DOI: 10.1016/j.ab.2003.12.023] [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] [Received: 06/27/2003] [Indexed: 11/23/2022]
Abstract
We have exploited three methods for discriminating single-nucleotide polymorphisms (SNPs) by detecting the incorporation or otherwise of labeled dideoxy nucleotides at the end of a primer chain using single-molecule fluorescence detection methods. Good discrimination of incorporated vs free nucleotide may be obtained in a homogeneous assay (without washing steps) via confocal fluorescence correlation spectroscopy or by polarization anisotropy obtained from confocal fluorescence intensity distribution analysis. Moreover, the ratio of the fluorescence intensities on each polarization channel may be used directly to discriminate the nucleotides incorporated. Each measurement took just a few seconds and was done in microliter volumes with nanomolar concentrations of labeled nucleotides. Since the confocal volumes interrogated are approximately 1fL and the reaction volume could easily be lowered to nanoliters, the possibility of SNP analysis with attomoles of reagents opens up a route to very rapid and inexpensive SNP detection. The method was applied with success to the detections of SNPs that are known to occur in the BRCA1 and CFTR genes.
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Affiliation(s)
- Charles R Twist
- Institute of Biological Sciences, Cledwyn Building, University of Wales, Aberystwyth SY23 3DD, Wales, UK
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Zhou GH, Shirakura H, Kamahori M, Okano K, Nagai K, Kambara H. A gel-free SNP genotyping method: bioluminometric assay coupled with modified primer extension reactions (BAMPER) directly from double-stranded PCR products. Hum Mutat 2004; 24:155-63. [PMID: 15241797 DOI: 10.1002/humu.20052] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Inexpensive, high-throughput genotyping methods are needed for analyzing human genetic variations. We have successfully applied the regular bioluminometric assay coupled with modified primer extension reactions (BAMPER) method to single-nucleotide polymorphism (SNP) typing as well as the allele frequency determination for various SNPs. This method includes the production of single-strand target DNA from a genome and a primer extension reaction coupled with inorganic pyrophosphate (PPi) detection by a bioluminometric assay. It is an efficient way to get accurate allele frequencies for various SNPs, while single-strand DNA preparation is labor intensive. The procedure can be simplified in the typing of SNPs. We demonstrate that a modified BAMPER method in which we need not prepare a single-strand DNA can be carried out in one tube. A PCR product is directly used as a template for SNP typing in the new BAMPER method. Generally, tremendous amounts of PPi are produced in a PCR process, as well as many residual dNTPs, and residual PCR primers remain in the PCR products, which cause a large background signal in a bioluminometric assay. Here, shrimp alkaline phosphatase (SAP) and E. coli exonuclease I were used to degrade these components prior to BAMPER detection. The specific primer extension reactions in BAMPER were carried out under thermocycle conditions. The primers were extended to produce large amounts of PPi only when their bases at 3'-termini were complementary to the target. The extension products, PPis, were converted to ATP to be analyzed using the luciferin-luciferase detection system. We successfully demonstrated that PCR products can be directly genotyped by BAMPER in one tube for SNPs with various GC contents. As all reactions can be carried out in a single tube, the method will be useful for realizing a fully automated genotyping system.
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Affiliation(s)
- Guo-Hua Zhou
- Hitachi, Ltd., Central Research Laboratory, Tokyo, Japan
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Mashima Y, Nagano M, Funayama T, Zhang Q, Egashira T, Kudho J, Shimizu N, Oguchi Y. Rapid quantification of the heteroplasmy of mutant mitochondrial DNAs in Leber's hereditary optic neuropathy using the Invader technology. Clin Biochem 2004; 37:268-76. [PMID: 15003728 DOI: 10.1016/j.clinbiochem.2003.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Revised: 11/20/2003] [Accepted: 11/20/2003] [Indexed: 10/26/2022]
Abstract
PURPOSE To quantify the degree of heteroplasmy of a mitochondrial DNA (mtDNA) mutation in Leber's hereditary optic neuropathy (LHON) a biplex Invader assay was applied. METHODS To determine the optimum condition for the Invader assay, mtDNAs were assayed in various amounts of total DNA in 1-4-h incubations at 63 degrees C. To evaluate the suitability of the Invader assay to detect the three mutations, G3460A, G11778A, and T14484C, 10 ng of DNAs from 224 patients with bilateral optic atrophy was assayed. To quantify mtDNA heteroplasmy, a standard curve of known mixture ratios of mutation against calculation by the Invader assay was constructed. Seventy-two of the 224 patients had one of the three mutations, which corresponded with the mutation detected earlier by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis. The percentages of mutant mtDNAs were calculated by the Invader assay in five heteroplasmic families, including 30 individuals with the G11778A mutation. The results were compared with those calculated earlier by labeled polymerase chain reaction followed by single-strand conformation polymorphism (PCR-SSCP) analysis. RESULTS In 1-8 ng of DNA, the fluorescence intensity increased near linearly during a 4-h assay. With more than 16 ng of DNA, the intensities were saturated even at the 2-h assay. A linear relationship was observed between the results obtained from separate mixtures and from the Invader assay analysis. Because two fluorescent intensities are not always the same, one of the two intensities was modified to adjust to that of the other. Complete concordance was observed between PCR-RFLP analysis and Invader assay genotyping for the 224 patients. Results of percentage of heteroplasmy in five LHON families obtained by the Invader assay were consistent with those by the PCR-SSCP analysis. CONCLUSIONS Invader assay is a simple, rapid, and reliable method of genotyping mtDNA mutations as well as quantifying heteroplasmy simultaneously under optimum conditions.
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Affiliation(s)
- Yukihiko Mashima
- Department of Ophthalmology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.
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Karvinen J, Elomaa A, Mäkinen ML, Hakala H, Mukkala VM, Peuralahti J, Hurskainen P, Hovinen J, Hemmilä I. Caspase multiplexing: simultaneous homogeneous time-resolved quenching assay (TruPoint) for caspases 1, 3, and 6. Anal Biochem 2004; 325:317-25. [PMID: 14751267 DOI: 10.1016/j.ab.2003.10.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Caspases are a group of cysteine proteases involved in apoptosis and inflammation. A multiparametric homogeneous assay capable of measuring activity of three different caspases in a single well of a microtiter plate is described. Different fluorescent europium, samarium, terbium, and dysprosium chelates were coupled to a caspase substrate peptide, their luminescence properties, were analyzed, and their function in a time-resolved fluorescence quenching-based caspase 3 assay was studied. Substrates for caspases 1, 2, 3, 6, and 8 and granzyme B were also synthesized and their specificities for different caspases were determined. By selecting suitable lanthanide chelates and substrates we developed a multiparametric homogeneous time-resolved fluorescence quenching-based assay for caspases 1, 3, and 6. The assay was capable of measuring the activity of both single caspases and a mixture of three caspases mixed in the same well.
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Affiliation(s)
- Jarkko Karvinen
- PerkinElmer Life and Analytical Sciences, Wallac Oy, P.O. Box 10, FIN-20101, Turku, Finland.
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Chen X, Sullivan PF. Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. THE PHARMACOGENOMICS JOURNAL 2004; 3:77-96. [PMID: 12746733 DOI: 10.1038/sj.tpj.6500167] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The large number of single nucleotide polymorphism (SNP) markers available in the public databases makes studies of association and fine mapping of disease loci very practical. To provide information for researchers who do not follow SNP genotyping technologies but need to use them for their research, we review here recent developments in the fields. We start with a general description of SNP typing protocols and follow this with a summary of current methods for each step of the protocol and point out the unique features and weaknesses of these techniques as well as comparing the cost and throughput structures of the technologies. Finally, we describe some popular techniques and the applications that are suitable for these techniques.
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Affiliation(s)
- X Chen
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA 23298-0424, USA.
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Powell N, Dudley E, Morishita M, Bogdanova T, Tronko M, Thomas G. Single nucleotide polymorphism analysis in the human phosphatase PTPrj gene using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2004; 18:2249-2254. [PMID: 15384144 DOI: 10.1002/rcm.1617] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Data derived from analysis of single nucleotide polymorphisms (SNPs) are being applied in many diverse fields, from medical studies of disease mechanisms and individual drug response, to population genetics for tracking migration and mixing of ancestral groups and also in forensic science for the identification of human remains and identification of individuals from bodily samples. All these applications have in common the need to generate data for multiple loci from large numbers of samples. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) is a promising platform for the generation of such data and we present a simple, flexible and robust technique for SNP determination. We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human phosphatase gene PTPrj, which has been implicated in the aetiology of colon, lung, breast and thyroid cancers. A nucleotide depletion primer extension assay using no commercial kits or dideoxyNTPs was used to genotype a panel of DNAs derived from thyroid cancer patients and normal volunteers. The results obtained were in perfect agreement with those generated via restriction fragment length polymorphism analysis. No significant association was noted between possession of either allelic variant and a disease state, but the technique was validated as simple, flexible and appropriate for application in this context. Furthermore, it was highly cost-effective and required minimal optimisation, rendering it ideal for this type of pilot study.
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Affiliation(s)
- Ned Powell
- Human Cancer Studies Group, Swansea Medical School, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, Wales, UK.
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Zhong XB, Reynolds R, Kidd JR, Kidd KK, Jenison R, Marlar RA, Ward DC. Single-nucleotide polymorphism genotyping on optical thin-film biosensor chips. Proc Natl Acad Sci U S A 2003; 100:11559-64. [PMID: 12975525 PMCID: PMC208797 DOI: 10.1073/pnas.1934783100] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) constitute the bulk of human genetic variation and provide excellent markers to identify genetic factors contributing to complex disease susceptibility. A rapid, sensitive, and inexpensive assay is important for large-scale SNP scoring. Here we report the development of a multiplex SNP detection system using silicon chips coated to create a thin-film optical biosensor. Allele-discriminating, aldehyde-labeled oligonucleotides are arrayed and covalently attached to a hydrazinederivatized chip surface. Target sequences (e.g., PCR amplicons) then are hybridized in the presence of a mixture of biotinylated detector probes, one for each SNP, and a thermostable DNA ligase. After a stringent wash (0.01 M NaOH), ligation of biotinylated detector probes to perfectly matched capture oligomers is visualized as a color change on the chip surface (gold to blue/purple) after brief incubations with an anti-biotin IgG-horseradish peroxidase conjugate and a precipitable horseradish peroxidase substrate. Testing of PCR fragments is completed in 30-40 min. Up to several hundred SNPs can be assayed on a 36-mm2 chip, and SNP scoring can be done by eye or with a simple digital-camera system. This assay is extremely robust, exhibits high sensitivity and specificity, and is format-flexible and economical. In studies of mutations associated with risk for venous thrombosis and genotyping/haplotyping of African-American samples, we document high-fidelity analysis with 0 misassignments in 500 assays performed in duplicate.
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Affiliation(s)
- Xiao-Bo Zhong
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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