SNP
한개의 염기서열의 차이를 이용하는 것을 말한다.
1번 개체 ACCATG
2번 개체 ACTATG
두 개체간의 염기서열의 차이를 이용하게 된다.
예를 들어 특정 질병에 잘 걸리는 집단과 잘 걸리지 않은 집단간의 유전자 차이를 비교, 질병의 원인을 규명혹은 마커 발견 할 때 유용하게 쓰이게 된다.
[Definition]
SNPs are single base pair positions in genomic DNA at which different
sequence alternatives (alleles) exist in normal individuals in some
population(s), wherein the least frequent allele has an abundance
of 1% or greater.
[Narrow scope]
Single base insertion/deletion variants (indels) would not
formally be considered to be SNPs.
[Pronunciation]
SNP (pronounced 'S' 'N' 'P' or 'SNiP')
[Characteristics of human SNPs]
Understand human DNA polymorphism, about 90% of which is
single nucleotide polymorphism (SNP)
SNPs could be bi-, tri-, or tetra-allelic polymorphisms.
However, in humans, tri-allelic and tetra-allelic SNPs are rare almost
to the point of non-existence, and so SNPs are sometimes simply
referred to as bi-allelic markers (or di-allelic)
The typical frequency with which one observes single base differences in genomic
DNA from two equivalent chromosomes is of the order of 1/1000 bp = 0.1%
cf) non-coding HLA regions show nucleotide diversity levels of 5–10%
[Application]
Population genetics and linkage disequilibrium :
The study of the genetic composition and inter-relationships between
populations. The major research tool it uses is DNA polymorphism.
Complex phenotypes and genome variation :
Risks of major common diseases such as cancer, cardiovascular disease,
mental illness, auto-immune states, and diabetes, are expected to be heavily
influenced by the patterns of SNPs one possesses in certain key susceptibility
genes yet to be identified.
SNP based association studies :
If a factor contributes an increased risk for disease occurrence, then that factor
should be found at higher frequency in individuals with that disease compared to
non-diseased controls
[Reference]
Brookes AJ, The essence of SNPs, Gene. 1999 Jul 8;234(2):177-86.
[Database and Tools]
http://biocc.ngic.re.kr/Variome/Biowiki/index.php/Databases_and_Tools