Single nucleotide polymorphism expression

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. 

Clifford, R., et al., "Expression-Based Genetic/Physical Maps of Single Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project," Genome Res., 10, 1259-1265 (2000). 

Biomolecular MS and in particular MALDI-TOF-MS (see Sections 2.1.22 and 2.2.1) permit the routine analysis of oligonucleotides up to 70-mers, intact nucleic acids, and the direct detection of DNA products with no primer labels with an increase in analysis speed and mass accuracy especially in contrast to traditional DNA separation techniques such as slab gels or capillary electrophoresis. Applications focus on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Precise and accurate gene expression measurements show relative and absolute numbers of target molecules determined independently of the number of PCR cycles. DNA methylation can be studied quantitatively. 

Misra A, Hong JY, Kim S (2007) Multiplex genotyping of cytochrome p450 single-nucleotide polymorphisms by use of MALDI-TOF mass spectrometry. Clin Chem 53 933-939 Moon YJ, Zhang S, Brazeau DA, Morris ME (2007) Effects of the flavonoid biochanin A on gene expression in primary human hepatocytes and human intestinal cells. Mol Nutr Food Res 51 317-323... 

Due to their functional involvement in specific molecular pathways, miRNAs have become interesting targets for therapeutic intervention. Examples of disease-related mechanisms affected by miRNAs include single-nucleotide polymorphisms (SNPs) in 3 UTR sequences (23, 24) or in miRNA genes (25, 26) that may affect normal protein expression and has been identified in association with heart failure (27) and cancer (25, 28). Chromosomal deletions and epigenetic changes involving miRNA also cause abnormal protein expression that is associated with malfunctions... 

Collins A, Lonjou C, Morton NE (1999) Genetic epidemiology of single-nucleotide polymorphisms [see comments]. Proc Natl Acad Sci U S A 96 15173-15177 Cordon-Cardo C, O Brien JP, Casals D, et al (1989) Multidrug-resistance gene (P-glyco-protein) is expressed by endothelial cells at blood-brain barrier sites. Proc Natl Acad Sci US A86 695-698... 

Fig. 2. Regulation of thymidylate synthase (TS) gene expression. Abbreviations.- TS (thymidylate synthase) USF-1 (upstream stimulating factor 1) USF-2 (upstream stimulating factor 2) SNP (single nucleotide polymorphism). (Reprinted with permission of El-Khoueiry et al. Pharmacogenomics and molecular biology of gastrointestinal cancers, Atlas of Gastrointestinal Cancers, Current Medicine Group, LLC, Philadelphia, 2007).

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