Single nucleotide polymorphism

DNA strand 1 differs from DNA strand 2 at a single base-pair location (a C/T polymorphism).

A single nucleotide polymorphism, or SNP (pronounced snip), is a DNA sequence variation occurring when a single nucleotide - A, T, C, or G - in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual). For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say that there are two alleles : C and T. Almost all common SNPs have only two alleles.

Within a population, SNPs can be assigned a minor allele frequency - the ratio of chromosomes in the population carrying the less common variant to those with the more common variant. It is important to note that there are variations between human populations, so a SNP allele that is common in one geographical or ethnic group may be much rarer in another. In the past, single nucleotide polymorphisms with a minor allele frequency of ≥ 1% (or 0.5%, etc.) were given the title "SNP," an unwieldy definition. With the advent of modern bioinformatics and a better understanding of evolution, this definition is no longer necessary.

Single nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions between genes. SNPs within a coding sequence will not necessarily change the amino acid sequence of the protein that is produced, due to degeneracy of the genetic code. A SNP in which both forms lead to the same polypeptide sequence is termed synonymous (sometimes called a silent mutation) - if a different polypeptide sequence is produced they are non-synonymous. SNPs that are not in protein-coding regions may still have consequences for gene splicing, transcription factor binding, or the sequence of non-coding RNA.

Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, and other agents. However, their greatest importance in biomedical research is for comparing regions of the genome between cohorts (such as with matched cohorts with and without a disease).

The study of single nucleotide polymorphisms is also important in crop and livestock breeding programs (see genotyping). See SNP genotyping for details on the various methods used to identify SNPs.

See also

• Single Base Extension
• Variome
• TaqMan
• Affymetrix
• International HapMap Project
• tag SNP

References

• Human Genome Project Information — SNP Fact Sheet
• Relation of SNP's with Cancer

External links

• NCBI resources - Introduction to SNPs from NCBI
• http://www.snpedia.com/ - SNPedia, a wiki devoted to SNPs, using Semantic MediaWiki
• The SNP Consortium LTD — SNP search
• NCBI dbSNP database — "a central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms"
• International HapMap Project — "a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals"
• Glovar Variation Browser — variation information in a genomic context
• WatCut — an online tool for the design of SNP-RFLP assays
• Restriction HomePage — a set of tools for DNA restriction and SNP detection, including design of mutagenic primers
• American Association for Cancer Research Cancer Concepts Factsheet on SNPs
• PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge Base, a resource for SNPs associated with drug response and disease outcomes.
• GEN-SNiP - Online tool that identifies polymorphisms in test DNA sequences.
• Variome.net - Human variation research using SNPs. Contains SNPs occurring on protein domains.
• Rules for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat
• HGNC Guidelines for Human Gene Nomenclature