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What is SNPs

A Single Nucleotide Polymorphism is a source variance in a genome. A SNP (βnip") is a single base mutation in DNA. SNPs are the most simple form and most common source of genetic polymorphism in the human genome (90% of all human DNA polymorphisms). There are two types of nucleotide base substitutions resulting in SNPs:

  • A transition substitution occurs between purines (A, G) or between pyrimidines (C, T). This type of substitution constitutes two thirds of all SNPs.
  • A transversion substitution occurs between a purine and a pyrimidine.

Sequence Variation

Sequence variation caused by SNPs can be measured in terms of nucleotide diversity, the ratio of the number of base differences between two genomes over the number of bases compared. This is approximately 1/1000 (1/1350) base pairs between two equivalent chromosomes.

Application:

pharmacogenomics
All aspects of pharmacogenomics require data from high-throughput genotyping, specifically the target population for a drug or the population of people who react poorly with the drug. Also, this type of research may lead to population specific treatments. The high cost of drug recalls have provided an initiative for advanced drug design involving drug-target validation studies as well as studies to predict adverse events and lack of efficacy.

A sample pharmacogenomic experiment may proceed as follows:
  • Define the drug response (phenotype) of interest
  • Accumulate patients/DNA/families
  • Identify candidate genes that might explain significant response variations
  • Identify polymorphisms in candidate genes
  • Relate the identified polymorphism to the phenotype
SNP Diagnostics

An individual's genotype can be determined and then analysed according to a haplotype map to determine the patient's disease risk or reception to different treatments.

SNPs in Functional Proteomics and Gene Therapy

SNP related functional proteomics involve the identification of functional SNPs that modify proteins and protein active sites structure and function. Functional proteomics is closely tied to modern (post-genomic) drug design and function SNP information helps to discover new therapeutic targets. Most interestingly, by developing a database of the modifications generated by functional (coding) SNPs in disease related proteins, "new compounds can be designed for correcting or enhancing the effects of those mutations in the population."
What are these compounds and how can knowledge of SNP effects be used to correct populations with undesirable SNPs or enhance populations by introducing the advantages of a desirable SNP? Aside from drugs, here are some interesting genomic therapies that may become more feasible as SNP information in the form of trees and maps become more detailed.