SNP analysis

The spotted array is also used for SNP analysis based upon primer extension labeling of oligonucleotide or cDNA probes. The advantage of... 

Kristensen, R., Berdal, K. G., and Holst-Jensen, A. (2006a). Simultaneous detection and identification of trichothecene- and moniliformin-producing Fusarium species based on multiplex SNP analysis. /. Appl. Microbiol, pp. 11. doi 10.1111/j.l365-2672.2006.03166.x. 

Another efficient way to empower SNP analysis is to use pathway information as scaffold to simultaneously test multiple polymorphisms. The underlying idea is that nucleotide variants may impact different components (genes) of the same pathway all affecting pathway functionality, which is what ultimately relates to the trait of interest. Individual variations may not have sufficient penetrance to reach significance that could be achieved by globally testing variation in all pathway components. This concept, developed initially... 

Single nucleotide polymorphism (SNP) analysis of the p53 cDNA from clinical samples was analyzed by CGE separation on a fused silica chip. No... 

Russom, A., Ahmadian, A., Andersson, H., Van Der Wijngaart, W., Lundeberg, J., Uhlen, M., Stemme, G., Nilsson, P., SNP analysis by allele-specific pyrosequenc-ing extension in a micromachined filter-chamber device. Micro Total Analysis Systems, Proceedings 5th pTAS Symposium, Monterey, CA, Oct. 21-25, 2001, 22-24. 

Honjo Y, Morisaki K, Huff LM, Robey RW, Hung J, Dean M, Bates SE. Single-nucleotide polymorphism (SNP) analysis in the ABC half-transporter ABCG2 (MXR/BCRP/ABCP1). Cancer Biol Ther 2002 1 696-702. 

Allen M, Divne AM. Universal tag arrays in forensic SNP analysis. Methods Mol Biol 2004 297 141-154. 

Mamellos G. High-throughput SNP analysis for genetic association studies. Curr Opin Drug Discov Dev 2003 6(3) 317-321. 

Figure 5 Ultrafast SNP analysis by primer extension and capillary electrophoresis. Upper panel electropherogram of the mutant homozygote (G-mutation) with the 19-mer primer peak and the 26-mer product Middle panel electropherogram of the wild type with the primer and the 35-mer product Lower panel electropherogram of the heterozygote with all three peaks (19-, 26-, and 35-mers). Conditions capillary, = 10 cm (effective) (L = 30 cm), i.d. 75 pm separation matrix and running buffer, 10% PVP (MW 1,300,000) in 1 xTBE applied voltage, 20 kV injection, 30 s/10 kV temperature, 30°C. (Reproduced with permission from Ref. 64.)...

Medintz I, Wong WW, Berti L, Shiow L, Tom J, Scherer J, et al. High-performance multiplex SNP analysis of three hemochromatosis-related mutations with capillary array electrophoresis microplates. Genome Res 2001 11 413-421. 

Microfluidic structures used to retain beads might then fulfill the dual purpose of holding back particles while allowing samples and reagents to be delivered. A first type of device is presented in Fig. 7 in which microspheres are confined either in a microchamber bordered by a leaky wall (Fig. 7A) [27] or by a pillar made wall (Fig. 7B) [28]. Such systems were used to perform single nucleotide polymorphism (SNP) analysis of the codon 72 of the gene of the anti-cancer p53 protein. 

Single-nucleotide polymorphism (SNP) analysis by fluorescence sensing and FRET... 

SNP analysis in homogeneous solutions Monolabeled uniprobes Fluorescent nucleosides in opposite position to the interrogation position (internal position of duplexes) Fluorescent sensing 2... 

SNP analysis with genomic DNA Monolabeled uniprobes F at the 5 -end - - free minor groove binder F FRET 34... 

DNA biosensors have a great potenticd for numerous applications which will include new improvements for the detection of single nucleotide polymorphisms (SNPs) analysis in personedized medicine, pathogenic organisms in the field of food control, and toxic pollutants in environmental monitoring. 

Several assays have been patented for mutation detection these are mainly designed for single-nucleotide polymorphism (SNP) analysis and use MALDI-TOF spectrometry (Invader , Sequazyme-PinPoint assay, MassARRAY , GOOD assay) all of which use PCR amplification, or require a high DNA concentration in the sample (Invader ). 

Methods for homogeneous SNP analysis in a closed-tube system differ greatly in their level of complexity (Figure 37-32). The number of oligonucleotides required varies from 2 to 8. The simpler techniques do not require probes at aU, although some of the more complex techniques require up to three labels or modifications on each probe. All of these methods use fluorescence and solution hybridization. Some of the methods that use melting analysis will detect more than two alleles if present those based on aHele-specific amplification or endpoint analysis are limited to two. 

The other main type of genotyping performed with oUgonucleotide arrays is SNP analysis, that is, the genotyping of biallelic single-nucleotide polymor-... 

These advantages taken together may be the reason that mass spectrometric based methods have been referred to as the gold standard for SNP analysis in a recent review on this topic [61]. 

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