Gene Variation Single Nucleotide Polymorphism

Strong correlation of a disease with a specific SNP is advantageous in clinical work because it is relatively easy to test for the affected individuals or carriers. A particular site 

TABLE 15.5 Common methods used to scan genes for mutations 

Southern blot (cDNA probe) Detect major deletions/rearrangements Labor intensive and requires pg of DNA 

Sequencing Detect all changes and mutations are Expensive/time-consuming and 

Heteroduplex gel mobility Simple, cheap Sequences of 200 bp only, limited sensitivity and does not reveal position of the change 

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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. 

As shown in Fig. 1.1, bioinformatics approaches in pharmacogenomics are conducted systematically. The lowest level in the system is at the molecular level. At this level, it is necessary to understand the detailed features of a gene and the relationship between genetic structure and function (see Subheading 1.2.1). These detailed features include sequence analytic information such as sequence retrieval and comparison, sequence variation information such as about single-nucleotide polymorphisms (SNPs), and sequence patterns that can correlate sequence structure to functional motifs. 

Bonnevie-Nielsen, V., Field, L. L., Lu, S., et al. (2005) Variation in antiviral 2, 5 -oligoade-nylate synthetase (2 5"AS) enzyme activity is controlled by a single-nucleotide polymorphism at a splice-acceptor site in the OASl gene. Am. J. Hum. Genet. 76,623-633. 

Here is a bit of a complication there is a lot of individual variation in the sense of human olfaction. Not everything smells the same to everyone. This holds both for the intensity of the perceived smeU as well as for its quality pleasant, floral, skunky, sweaty, or no odor at all. Andreas Keller has recently demonstrated that some significant part of this individual variation in the sense of smell derives from genetic variation in human odorant genes. Specifically, two single nucleotide polymorphisms (SNPs), leading to two amino acid substitutions in an odorant receptor, have dramatic affects on the perception of the odor of androstenone, a steroid derived from testosterone. 

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