Nucleotide polymorphisms, single

Phred reads and identifies DNA sequence trace data (bases), assigns quality values to the bases, and writes the base identities and quality values to output files. It uses Fourier methods, to examine the base traces (chromatographic peaks or profiles) in the region where a base is anticipated, that is, it determines where the, peak would be centered if there were no distortions or other factors shifting the peaks from their true locations. 

The approach taken by the private Celera group is somewhat different. They bypass the use of BAG libraries of long DNA pieces. Instead they break up the entire genome info fragments only 2000 to 10,000 nt long and sequence each of these, in chunks of up to about 700 bases (the resolution limit of the instruments). If we have 3 billion bases to worry about, this means a lot of pieces to sort out and assemble in the proper order (actually, only a portion of those are sorted, but it is still a lot). Powerful computers do the sorting to put the puzzle pieces together. 

To more rapidly process these millions of pieces, the whole operation is done automatically, performing separations by capillary electrophoresis, which has higher resolving power and is faster than gel electrophoresis. Detection is done by passing a laser beam through the eluting drops at the ends of multiple capillaries. The public consortium has largely switched to this instrument as well (the ABI Model 3700). 

There is controversy about which approach provides more accurate results. Both groups are continuing on filling the remaining gaps (remember, only 89% of the genes were initially determined). 

SNPs are what differentiate all of us. They constitute 0.1% of the genes. 

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Allele variant forms oftheDNA sequence at a specified locus. For example, alleles at a single-nucleotide polymorphism (SNP) are characterized by the nucleotide that is changing. The combination of two alleles at a locus constitutes a genotype. 

Analysing single nucleotide polymorphisms to hunt for genetic sources of diseases... 

Protein-protein interactions predicted on the sequence level can be studied in more detail on the structure level. Single Nucleotide Polymorphisms can be mapped on 3D structures of proteins in order to elucidate specific structural causes of disease. 

Single-Nucleotide Polymorphism P450 Mono-Oxygenase System... 

Single Nucleotide Polymorphisms (SNPs) are single base pair positions in genomic DNA at which normal individuals in a given population show different sequence alternatives (alleles) with the least frequent allele having an abundance of 1% or greater. SNPs occur once every 100-300 bases and are hence the most common genetic variations. 

Bond C, LaForge KS, Tian M, et al Single-nucleotide polymorphism in the human mu opioid receptor gene alters beta-endorphin binding and activity possible implications for opiate addiction. Proc Natl Acad Sci U S A 95 9608-9613, 1998 Borron SW, Monier C, Risede P, et al Flunitrazepam variably alters morphine, bu-prenorphine, and methadone lethality in the rat. Hum Exp Toxicol 21 399-603, 2002... 

The life sciences domain task force (LSR DTP) has several working groups architecture and road map, biochemical pathways, cheminformatics, gene expression, sequence analysis, and single nucleotide polymorphisms. 

SNP Single nucleotide polymorphism. Refers to the fact that single nucleotide genetic variation in genome sequence exists at discrete loci throughout the chromosomes. Measurement of allelic SNP differences is useful for gene mapping studies. 

Single nucleotide polymorphisms Single base-pair changes that are inherited as mendelian traits and might associate with a trait such as susceptibility to disease. 

Genetic data also support a role for CCR2 in atherosclerosis. The human CCR2 gene has a single nucleotide polymorphism (SNP) that results in a Val... 

Walters, J. Muhammad, W. Fox, K. F. Fox, A. Xi, R. D. Creek, C. Pirisi, L. Geno-typing single nucleotide polymorphisms using intact PCR products by electrospray quadrupole mass spectrometry. Rapid Comm. Mass Spectrom. 2001,15,1752-1759. 

Yamamoto, K., Narukawa, J., Kadono-Okuda, K. et al. 2006. Construction of a single nucleotide polymorphism linkage map for the silkworm, Bombyx mori, based on bacterial artificial chromosome end sequences. Genetics, 173(1) 151—161. 

Considerable amounts of quenching of the acridone emissions by guanine in the DNA occurred when guanine was close to acridone, which can be applied as a quencher-free probe (no additional quencher is required) for the detection of a special sequence of DNA. The DNA bearing acridone at the C5 position of inner thymidine could distinguish the opposite T-T base mismatch, while enhancement of discrimination ability is needed for the practical use of single nucleotide polymorphism (SNP) typing. 

Recently, the presence of single nucleotide polymorphisms (SNPs) has been reported for several types of transporter. Extensive studies have been performed on the SNPs of OATP2 [100, 101], and the SNPs identified in African- and European-Americans are indicated in Fig. 12.3. Moreover, the frequency of SNPs differed among the African-American, European-Americans and Japanese, indicating the presence of an ethnic difference in the allelic mutation of this transporter [100, 101]. In addition, some of the mutations were associated with reduced transporter function and/or abnormalities in membrane targeting [100, 102] (Fig. 12.3). It is... 

Fig. 12.4. Single nucleotide polymorphisms in OATP2 gene found in African- and European Americans. Asterisks represent the mutations associated with the altered transport function. (Prepared from data reported in Ref. [100].)...

Suzuki, H., Sugiyama, Y., Single nucleotide polymorphisms in Multidrug Resistance Associated Protein... 

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