SNP

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'''Definition:'''
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[[Image:dna-SNP.svg|thumb|DNA strand 1 differs from DNA strand 2 at a single base-pair location (a C/T polymorphism).]]
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SNP or so called single nucleotide polymorphism are single nucleotide changes occuring in DNA.
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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, AAGC'''C'''TA to AAGC'''T'''TA, 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.
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These are commonly also referred to as Snips.
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These are like genetic landmarks in the genome which can beused to study the evolutionary trend both intra and inter specifically.
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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.
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Along with this these can also be visualised to study the association of a person with disease susceptibility.
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This is simply the lesser of the two allele frequencies for single nucleotide polymorphisms.
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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.
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== "SNP" ==
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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", an unwieldy definition.
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 +
Some used "mutation" to refer to variations with low allele frequency.
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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.
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== Types of SNPs ==
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{| class="infobox"
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|-
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! Types of SNPs
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|-
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|
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* Non-coding region
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* Coding region
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** Synonymous
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** Nonsynonymous
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*** Missense
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*** Nonsense
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|}
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Single nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions between genes.
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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.
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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''.
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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 primature stop codon.
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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.
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== Use and importance of SNPs ==
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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. 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).
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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.
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== Examples ==
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Example SNPs are rs6311 and rs6313 in the HTR2A gene.
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A SNP in the ''F5'' gene causes a hypercoagulability disorder with the variant Factor V Leiden.
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An example of a triallelic SNP is rs3091244.
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== Databases ==
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Like for gene there are also bioinformatics databases for SNPs.
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''dbSNP'' is a SNP database from National Center for Biotechnology Information (NCBI).
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''SNPedia'' is a wiki-style database from a private company.
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The ''OMIM'' database describes the association between polymorphisms and, e.g., diseases.
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== Nomenclature ==
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The nomenclature for SNPs can be confusing, several variations can exist for the individual SNP, and consensus seems not to have occured.
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One recommendation may write SNPs with prefix, dot, greater than sign and nucleotide or amino acids, e.g., c.76A>T.
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==References==
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*[http://www.nature.com/nrg/journal/v5/n2/glossary/nrg1270_glossary.html]
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*[http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml Human Genome Project Information] — SNP Fact Sheet
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*[http://nci.nih.gov/cancertopics/understandingcancer/geneticvariation/Slide1 Relation of SNP's with Cancer]
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==External links==
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*[http://www.ncbi.nlm.nih.gov/About/primer/snps.html NCBI resources] - Introduction to SNPs from NCBI
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*[http://snp.cshl.org/ The SNP Consortium LTD] — SNP search
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*[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"
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*[http://hapmap.org/ International HapMap Project] — "a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals"
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*[http://www.1000genomes.org/ 1000 Genomes Project] -  A Deep Catalog of Human Genetic Variation
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*[http://www.glovar.org/ Glovar Variation Browser] — variation information in a genomic context
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*[http://watcut.uwaterloo.ca/watcut/watcut/template.php WatCut] — an online tool for the design of SNP-RFLP assays
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*[http://bioinfo.iconcologia.net/index.php?module=Snpstats SNPStats] — SNPStats, a web tool for analysis of genetic association studies
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*[http://insilico.ehu.es/restriction Restriction HomePage] — a set of tools for DNA restriction and SNP detection, including design of mutagenic primers
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*[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]
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*[http://www.pharmgkb.org PharmGKB] - The Pharmacogenetics and Pharmacogenomics Knowledge Base, a   resource for SNPs associated with drug response and disease outcomes.
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*[http://www.argusbio.com/sooryakiran/gensnip/gensnip.php GEN-SNiP] - Online tool that identifies polymorphisms in test DNA sequences.
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*[http://www.informatics.jax.org/mgihome/nomen/gene.shtml Rules for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat]
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*[http://www.gene.ucl.ac.uk/nomenclature/guidelines.html HGNC Guidelines for Human Gene Nomenclature]

Revision as of 08:45, 16 September 2008

Image:Dna-SNP.svg
DNA strand 1 differs from DNA strand 2 at a single base-pair location (a C/T 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. 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.

Contents

"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", 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.

Types of SNPs

Types of SNPs
  • Non-coding region
  • Coding region
    • Synonymous
    • Nonsynonymous
      • Missense
      • Nonsense

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 primature 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. 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.

Databases

Like for gene 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 the individual SNP, and consensus seems not to have occured. One recommendation may write SNPs with prefix, dot, greater than sign and nucleotide or amino acids, e.g., c.76A>T.


References

External links

Retrieved from "http://277988.efsst.group/drugpedia/index.php/SNP"