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Cordeiro M, Giestas L, Lima JC, Baptista P. Coupling an universal primer to SBE combined spectral codification strategy for single nucleotide polymorphism analysis. J Biotechnol 2013; 168:90-4. [PMID: 23942375 DOI: 10.1016/j.jbiotec.2013.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 07/31/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
We previously reported a strategy that combines Förster resonance energy transfer (FRET) based spectral codification with a single base extension (SBE) reaction for single nucleotide sequence discrimination in solution. This strategy is capable of unequivocally detect the allele variants present in solution. To extend the use of this tool to any locus of interest, it would be required the development of an universal approach capable of combining a sequence specific SBE primer to an universal sequence labeled and optimized for spectral codification. Here, we extend this concept to a general strategy by means of a labeled universal oligonucleotide primer (donor), a sequence specific primer that allows for incorporation of the complementary acceptor labeled ddNTP, which allows discrimination the allele variant in the sample via the unambiguous FRET signature of the donor/acceptor pair.
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Affiliation(s)
- Mílton Cordeiro
- CIGMH, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal; REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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2
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Gehring I, Geider K. Differentiation of Erwinia amylovora and Erwinia pyrifoliae Strains with Single Nucleotide Polymorphisms and by Synthesis of Dihydrophenylalanine. Curr Microbiol 2012; 65:73-84. [DOI: 10.1007/s00284-012-0116-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 02/28/2012] [Indexed: 10/28/2022]
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Detection of ERCC1 118 Polymorphisms in Non-small-cell Lung Cancer by an Improved Fluorescence Polarization Assay. ACTA ACUST UNITED AC 2010; 19:164-8. [DOI: 10.1097/pdm.0b013e3181c14814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wheeler DS, Wong HR, Shanley TP. Genetic Polymorphisms in Critical Care and Illness. SCIENCE AND PRACTICE OF PEDIATRIC CRITICAL CARE MEDICINE 2009. [PMCID: PMC7123127 DOI: 10.1007/978-1-84800-921-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Derek S. Wheeler
- Medical Center, Div. of Critical Care Medicine, Cincinnati Children's Hospital, Burnet Avenue 3333, Cincinnati, 45229 U.S.A
| | - Hector R. Wong
- Medical Center, Div. of Critical Care Medicine, Cincinnati Children's Hospital, Burnet Avenue 3333, Cincinnati, 45229 U.S.A
| | - Thomas P. Shanley
- C.S. Mott Children's Hospital , Pediatric Critical Care Medicine , University of Michigan, E. Medical Center Drive 1500, Ann Arbor, 48109-0243 U.S.A
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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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Di Gaetano C, Crobu F, Guarrera S, Polidoro S, Gasparini M, Underhill PA, Matullo G, Piazza A. The TDI-FP assay in human Y chromosome SNP haplotyping. ACTA ACUST UNITED AC 2005; 8:400-3. [PMID: 15684870 DOI: 10.1089/gte.2004.8.400] [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: 11/13/2022]
Abstract
One of the many commercial technologies for genotyping single nucleotide polymorphisms (SNPs) is template direct dye-terminator incorporation with fluorescence-polarization (TDI-FP assay). It is a single-base extension assay followed by reading the fluorescence polarization values in an appropriate instrument. We have evaluated the suitability of the TDI-FP technique to detect haploid uniparentally inherited DNA polymorphisms on the nonrecombining portion of the Y chromosome. A sample of 47 individuals has been genotyped for 8 Y chromosome biallelic markers. The SNP typing was blindly duplicated by the denaturing high-performance liquid chromatography (DHPLC) technique for comparison. In the cases under examination the TDI-FP assay was able to resolve an allelic state fully. Such a result showed 100% concordance indicating how efficiently the TDI assay can be used to genotype Y chromosome DNA SNPs. However, a percentage of indeterminate genotypes remained unresolved by simple visual inspection: it varied from 0% to 11% depending on the SNP locus and on the success of amplification. This is consistent with previous findings. A maximum likelihood classificatory analysis allowed some of the indeterminate genotypes to be assigned and some potentially misclassified samples to be identified. Their percentage remains relatively high despite retyping and therefore alternative techniques for these noncompliant situations are required.
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Affiliation(s)
- C Di Gaetano
- Dipartimento di Genetica, Biologia e Biochimica, Università di Torino, 10126 Torino, Italy
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Lopez-Crapez E, Bazin H, Chevalier J, Trinquet E, Grenier J, Mathis G. A separation-free assay for the detection of mutations: Combination of homogeneous time-resolved fluorescence and minisequencing. Hum Mutat 2005; 25:468-75. [PMID: 15832307 DOI: 10.1002/humu.20162] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Single nucleotide primer extension reaction has been widely used in DNA testing, and several detection methods based on this core allelic discrimination have been developed. Most of the reported formats are based on a two step protocol involving first, a liquid phase extension reaction, then a physical separation process (chromatography, electrophoresis, capture on solid support, mass spectrometry). Here we describe a new strategy based on homogeneous time-resolved fluorescence (HTRF), which does not involve any separation process and which allows a simple "mix and measure" protocol. In this approach, a 5'-(europium) cryptate-labeled primer is elongated by a biotinylated dideoxynucleoside-triphosphate, followed by the addition of a streptavidin-acceptor conjugate, which gives rise to a long-life fluorescence resonance energy transfer (FRET) signal between the cryptate donor and the acceptor. We present the development of HTRF technology as applied to the diagnosis of tumor suppressor gene p53 (TP53) mutations, and its application to the analysis of genomic DNA from human tumoral samples. The sensitivity of the reported method is compared to the corresponding fluorescent polarization assay.
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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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Saleh M, Vaillancourt JP, Graham RK, Huyck M, Srinivasula SM, Alnemri ES, Steinberg MH, Nolan V, Baldwin CT, Hotchkiss RS, Buchman TG, Zehnbauer BA, Hayden MR, Farrer LA, Roy S, Nicholson DW. Differential modulation of endotoxin responsiveness by human caspase-12 polymorphisms. Nature 2004; 429:75-9. [PMID: 15129283 DOI: 10.1038/nature02451] [Citation(s) in RCA: 296] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Accepted: 03/01/2004] [Indexed: 12/14/2022]
Abstract
Caspases mediate essential key proteolytic events in inflammatory cascades and the apoptotic cell death pathway. Human caspases functionally segregate into two distinct subfamilies: those involved in cytokine maturation (caspase-1, -4 and -5) and those involved in cellular apoptosis (caspase-2, -3, -6, -7, -8, -9 and -10). Although caspase-12 is phylogenetically related to the cytokine maturation caspases, in mice it has been proposed as a mediator of apoptosis induced by endoplasmic reticulum stress including amyloid-beta cytotoxicity, suggesting that it might contribute to the pathogenesis of Alzheimer's disease. Here we show that a single nucleotide polymorphism in caspase-12 in humans results in the synthesis of either a truncated protein (Csp12-S) or a full-length caspase proenzyme (Csp12-L). The read-through single nucleotide polymorphism encoding Csp12-L is confined to populations of African descent and confers hypo-responsiveness to lipopolysaccharide-stimulated cytokine production in ex vivo whole blood, but has no significant effect on apoptotic sensitivity. In a preliminary study, we find that the frequency of the Csp12-L allele is increased in African American individuals with severe sepsis. Thus, Csp12-L attenuates the inflammatory and innate immune response to endotoxins and in doing so may constitute a risk factor for developing sepsis.
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Affiliation(s)
- Maya Saleh
- Department of Biochemistry, Molecular Biology and Pharmacology, Merck Frosst Centre for Therapeutic Research, Montreal, Quebec H9H 3L1, Canada
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Freeman BD, McLeod HL. Challenges of implementing pharmacogenetics in the critical care environment. Nat Rev Drug Discov 2004; 3:88-93. [PMID: 14708023 DOI: 10.1038/nrd1285] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bradley D Freeman
- Department of Surgery, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8109, St Louis, Missouri 63110, USA.
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