Single-nucleotide polymorphism
From ISOGG Wiki
A single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation occurring when a single nucleotide adenine (A), thymine (T), cytosine (C), or guanine (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.
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Types of SNPs
Single nucleotides may be changed (substitution), removed (deletions) or added (insertion) to a polynucleotide sequence. 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 ribonucleic acid (RNA).
Use and importance of SNPs
Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, medication, 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 matched cohorts with and without a disease).
Further reading
- Human Genome Project Information — SNP Fact Sheet
- NCBI resources — Introduction to SNPs from NCBI
Useful websites, databases and tools
- The ISOGG SNP index
- The SNP Consortium LTD — SNP search
- NCBI dbSNP database — "a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms"
- SNPedia - a wiki devoted to the medical consequences of DNA variations, including software to analyze personal genomes
- International HapMap Project — "a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals"
- HGVbaseG2P — The Human Genome Variation database of Genotype-to-Phenotype information
- 1000 Genomes Project — A Deep Catalog of Human Genetic Variation
- SIFT — "An online tool that predicts on the effect of SNPs on protein function"
- WatCut — an online tool for the design of SNP-RFLP assays
- SNPStats — SNPStats, a web tool for analysis of genetic association studies
- Restriction HomePage — a set of tools for DNA restriction and SNP detection, including design of mutagenic primers
- PharmGKB — The Pharmacogenetics and Pharmacogenomics Knowledge Base, a resource for SNPs associated with drug response and disease outcomes.
- Online tool that predicts on the effects of SNPs on protein function
- Rules for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat
- HGNC Guidelines for Human Gene Nomenclature
- DNA Heritage masterclass on SNPs and haplogroups
