Single nucleotide polymorphism


Single nucleotide polymorphism

A single nucleotide polymorphism (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 lowest allele frequency at a locus that is observed in a particular population. This is simply the lesser of the two allele frequencies for single nucleotide polymorphisms [1] .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.

"SNP"

In the past, SNPs with a minor allele frequency of less than or equal to 1% (or 0.5%, etc.) were given the title "SNP", [E.g., Cite web
title = Methods for Discovering and Scoring Single Nucleotide Polymorphisms
url = http://www.genome.gov/10001029
publisher = National Human Genome Research Institute
] an unwieldy definition.Some used "mutation" to refer to variations with low allele frequency.With the advent of modern bioinformatics and a better understanding of evolution, this definition is no longer necessary, e.g., a database such as dbSNP includes "SNPs" that have lower allele frequency than one percent. [Cite news
url = http://www.ncbi.nlm.nih.gov/Web/Newsltr/Summer02/snp.html
title = SNP Population Grows at NCBI
publisher = NCBI
work = NCBI News
]

Types of SNPs

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 "nonsynonymous".A nonsynonymous change may either be missense or "nonsense", where a missense change results in a different amino acid, while a nonsense change results in a premature stop codon.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.

Use and importance of SNPs

Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, and other agents. SNPs are also thought to be key enablers in realizing the concept of personalized medicine. [cite news | author=Bruce Carlson | title=SNPs — A Shortcut to Personalized Medicine
url=http://www.genengnews.com/articles/chitem.aspx?aid=2507 | work=Genetic Engineering & Biotechnology News
publisher=Mary Ann Liebert, Inc. | page=12 | date=2008-06-15 | accessdate=2008-07-06
quote=(subtitle) Medical applications are where the market's growth is expected
] 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.

Examples

Example SNPs are rs6311 and rs6313 in the HTR2A gene.A SNP in the "F5" gene causes a hypercoagulability disorder with the variant Factor V Leiden.An example of a triallelic SNP is rs3091244. [Cite journal
author = Akihiko Morita, Tomohiro Nakayama, Nobutaka Dobac, Shigeaki Hinoharac, Tomohiko Mizutania and Masayoshi Soma
title = Genotyping of triallelic SNPs using TaqMan® PCR
journal = Molecular and Cellular Probes
volume = 21
issue = 3
month = june
year = 2007
pages = 171–176
]

Databases

As there are for genes there are also bioinformatics databases for SNPs."dbSNP" is a SNP database from National Center for Biotechnology Information (NCBI)."SNPedia" is a wiki-style database from a private company.The "OMIM" database describes the association between polymorphisms and, e.g., diseases.

Nomenclature

The nomenclature for SNPs can be confusing: several variations can exist for an individual SNP and consensus has not yet been achieved. One approach is to write SNPs with a prefix, period and greater than sign showing the wild-type and altered nucleotide or amino acid; for example, c.76A>T. [Cite web
author = J.T. Den Dunnen
title = Recommendations for the description of sequence variants
date = 2008-02-20
accessdate = 2008-09-05
url = http://www.hgvs.org/mutnomen/recs.html
publisher = Human Genome Variation Society
] [Cite journal
author = Johan T. den Dunnen & Stylianos E. Antonarakis
title = Mutation Nomenclature Extensions and Suggestions to Describe Complex Mutations: A Discussion
journal = Human Mutation
volume = 15
pages = 7–12
year = 2000
url = http://www3.interscience.wiley.com/cgi-bin/fulltext/68503056/PDFSTART
] [Cite journal
author = Shuji Ogino, Margaret L. Gulley, Johan T. den Dunnen, Robert B. Wilson and the Association for Molecular Pathology Training and Education Committee
title = Standard Mutation Nomenclature in Molecular Diagnostics
journal = The Journal of Molecular Diagnostics
year = 2007
volume = 9
issue= 1
doi = 10.2353/jmoldx.2007.060081
]

See also

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

Notes

References

* [http://www.nature.com/nrg/journal/v5/n2/glossary/nrg1270_glossary.html]
* [http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml Human Genome Project Information] — SNP Fact Sheet
* [http://nci.nih.gov/cancertopics/understandingcancer/geneticvariation/Slide1 Relation of SNP's with Cancer]

External links

* [http://www.ncbi.nlm.nih.gov/About/primer/snps.html NCBI resources] - Introduction to SNPs from NCBI
* [http://snp.cshl.org/ The SNP Consortium LTD] — SNP search
* [http://www.ncbi.nlm.nih.gov/projects/SNP/ NCBI dbSNP database] — "a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms"
* [http://hapmap.org/ International HapMap Project] — "a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals"
* [http://www.1000genomes.org/ 1000 Genomes Project] - A Deep Catalog of Human Genetic Variation
* [http://www.glovar.org/ Glovar Variation Browser] — variation information in a genomic context
* [http://watcut.uwaterloo.ca/watcut/watcut/template.php WatCut] — an online tool for the design of SNP-RFLP assays
* [http://bioinfo.iconcologia.net/index.php?module=Snpstats SNPStats] — SNPStats, a web tool for analysis of genetic association studies
* [http://insilico.ehu.es/restriction Restriction HomePage] — a set of tools for DNA restriction and SNP detection, including design of mutagenic primers
* [http://www.aacr.org/home/public--media/for-the-media/fact-sheets/cancer-concepts/snps.aspx American Association for Cancer Research Cancer Concepts Factsheet on SNPs]
* [http://www.pharmgkb.org PharmGKB] - The Pharmacogenetics and Pharmacogenomics Knowledge Base, a resource for SNPs associated with drug response and disease outcomes.
* [http://www.argusbio.com/sooryakiran/gensnip/gensnip.php GEN-SNiP] - Online tool that identifies polymorphisms in test DNA sequences.
* [http://www.informatics.jax.org/mgihome/nomen/gene.shtml Rules for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat]
* [http://www.gene.ucl.ac.uk/nomenclature/guidelines.html HGNC Guidelines for Human Gene Nomenclature]


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