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Single-nucleotide polymorphism

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DNA molecule 1 differs from DNA molecule 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 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. 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.

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 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.[1] 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.

They are usually biallelic and thus easily assayed.[2] SNPs do not necessarily function individually, rather, they work in coordination with other SNPs to manifest a disease condition as has been seen in osteoporosis[3]See

Examples

  • rs6311 and rs6313 are SNPs in the HTR2A gene on human chromosome 13.
  • A SNP in the F5 gene causes a hypercoagulability disorder with the variant Factor V Leiden.
  • rs3091244 is an example of a triallelic SNP in the CRP gene on human chromosome 1.[4]
  • TAS2R38 codes for PTC tasting ability, and contains 6 annotated SNPs.[5]

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 hybrid organization. The OMIM database describes the association between polymorphisms and, e.g., diseases in text form, HGMD® the Human Gene Mutation Database provides gene mutations causing or associated with human inherited diseases and functional SNPs, while HGVbaseG2P allows users to visually interrogate the actual summary-level association data.

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.[6][7][8]

See also

Notes

  1. ^ Bruce Carlson (2008-06-15). "SNPs — A Shortcut to Personalized Medicine". Genetic Engineering & Biotechnology News. Mary Ann Liebert, Inc. p. 12. Retrieved 2008-07-06. (subtitle) Medical applications are where the market's growth is expected
  2. ^ R. et al. Sachidanandam. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409:928–933, 2001
  3. ^ Monica Singh, Puneetpal Singh, Pawan Kumar Juneja, Surinder Singh, Taranpal Kaur (2010) SNP-SNP interactions within APOE gene influence plasma lipids in postmenopausal osteoporosis. Rheumatol Int
  4. ^ Morita, A; Nakayama, T; Doba, N; Hinohara, S; Mizutani, T; Soma, M (2007). "Genotyping of triallelic SNPs using TaqMan PCR". Molecular and Cellular Probes. 21 (3): 171–176. doi:10.1016/j.mcp.2006.10.005. PMID 17161935. {{cite journal}}: More than one of |author= and |last1= specified (help); Unknown parameter |month= ignored (help)
  5. ^ Prodi DA, Drayna D, Forabosco P, Palmas MA, Maestrale GB, Piras D, Pirastu M, Angius A (2004). "Bitter taste study in a sardinian genetic isolate supports the association of phenylthiocarbamide sensitivity to the TAS2R38 bitter receptor gene". Chem. Senses. 29 (8): 697–702. doi:10.1093/chemse/bjh074. PMID 15466815.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ J.T. Den Dunnen (2008-02-20). "Recommendations for the description of sequence variants". Human Genome Variation Society. Retrieved 2008-09-05.
  7. ^ Johan T. den Dunnen & Stylianos E. Antonarakis (2000). "Mutation Nomenclature Extensions and Suggestions to Describe Complex Mutations: A Discussion". Human Mutation. 15 (1): 7–12. doi:10.1002/(SICI)1098-1004(200001)15:1<7::AID-HUMU4>3.0.CO;2-N. PMID 10612815.
  8. ^ Ogino, S; Gulley, ML; Den Dunnen, JT; Wilson, RB; Association For Molecular Patholpogy Training And Education, Committee (2007). "Standard Mutation Nomenclature in Molecular Diagnostics". The Journal of Molecular Diagnostics. 9 (1): 1–6. doi:10.2353/jmoldx.2007.060081. PMC 1867422. PMID 17251329. {{cite journal}}: More than one of |author= and |last1= specified (help)

References

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