Single nucleotide polymorphisms
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.
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. Usually one will want to refer to SNPs with a minor allele frequency of ≥ 1% (or 0.5% etc.), rather than to "all SNPs" (a set so large as to be unwieldy). It is important to note that there are variations between human populations, so a SNP that is common enough for inclusion in one geographical or ethnic group may be much rarer in another.
SNPs may fall within coding sequences of genes, noncoding 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.
SNPs make up 90% of all human genetic variations, and SNPs with a minor allele frequency of ≥ 1% occur every 100 to 300 bases along the human genome, on average, where two of every three SNPs substitute cytosine with thymine.
Variations in the DNA sequences of humans can affect how humans develop diseases, respond to pathogens, chemicals, drugs, etc. As a consequence SNPs are of great value to biomedical research and in developing pharmacy products. Because SNPs are inherited and 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).
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, existing SNPs are most easily studied using microarrays. Microarrays allow the simultaneous testing of up to hundreds of thousands of separate SNPs and are quickly screened by computer.
- NCBI resources - Introduction to SNPs from NCBI
- 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.