A Single Nucleotide Polymorphism or SNP (pronounced snip) is a DNA sequence variation, occurring when a single nucleotide: adenine (A), thymine (T), cytosine (C) or guanine (G) - in the genome differs between members of the species. For example, two sequenced DNA fragments from different organisms, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. A variation must occur in at least 1% of the population to be considered a SNP.
SNPs may fall within coding sequences (CDS) of genes or between genes (intergenic regions). SNPs within a CDS change the codon, which may or may not change the amino acid in the protein sequence. The former may constitute different alleles. The latter are called silent mutations and typically occur in the third position of the codon (called the wobble position).
SNPs make up 90% of all human genetic variations, and occur every 100 to 300 bases along the human genome, on average, where two of every three SNPs substitute cytosine (C) with thymine (T). Variations in the DNA sequences of humans can affect how humans respond to diseases, bacteria, viruses, chemicals, drugs, etc.
SNPs are of great value to biomedical research and in developing pharmacy products. Because SNPs do not change much from generation to generation, following them during population studies is straightforward. They are also used in some forms of genealogical DNA testing.
The study of SNPs is also important in crop and livestock breeding programs (see genotyping).
Detection
A convenient method for detecting SNPs is restriction fragment length polymorphism (SNP-RFLP). If one allele contains a recognition site for a restriction enzyme while the other does not, digestion of the two alleles will give rise to fragments of different length. Currently, the study of existing SNPs are most easily studied using microarrays. Microarrays allow the simultaneous testing of over a thousand separate SNPs and are quickly screened by computer.
Several other ways to detect SNP's are mentioned in an article published in October 2005 in Nature by the International HapMap Consortium.
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