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Single Nucleotide Polymorphisms SNPs

Background on Single Nucleotide Polymorphisms (SNPs)

Single Nucleotide Polymorphisms, or SNPs (pronounced "snips"), are small genetic changes or variations such as a one nucleotide change, that can occur within a DNA sequence. The genetic code is specified by the four nucleotides: A (adenine), C (cytosine), G (guanine) and T (thymine). SNP polymorphisms occur when a single nucleotide, such as an A, replaces T in the DNA segment GGTAC  to GGAAC. 

SNPs make up more than 90% of all human genetic variations.  Interestingly, SNPs with a minor allele frequency of ≥ 1% occur every 100 to 300 bases in the chromosomes of the human genome, on average, where about 66% of SNPs are thymine to cytosine substitutions.

SNPs occur in the human population more than 1 percent of the time. Due to the fact that about only 3 to 5 percent of a person's DNA codes for the production of proteins, most SNPs are located outside of protein coding regions. However, SNPs that are found within coding sequences are of much interest for investigators as these SNPs possibly can alter the biological function of a protein. With the recent advances in technology such as the applications of microarrays to SNP detection and analysis, coupled with the unique ability of these genetic variations to facilitate gene identification, there has been a recent explosion of interest in SNP discovery and analysis.

 

Molecular Methods of Single Nucleotide Polymorphism SNP Detection

SNP PCR for Single Nucleotide Polymorphism Detection

Tetra primer ARMS PCR is used for SNP detection. Real-time PCR is also being used to carefully assess and confirm SNPs. For example, TaqMan® SNP Genotyping Assays are being used to analyze SNPs using PCR.  

SNP Microarrays for SNP Analysis

With the recent application of microarrays to the analysis and detection of SNPs, high throughput analysis of hundreds and now even thousands of SNPs is possible.  Therefore, microarrays allow the quickest way to study SNPs as computers can analyze all the microarray data obtained by array.

Detection of SNPs with dHPLC

Denaturing high-performance liquid chromatography, termed DHPLC for short is a very fast and convenient methods to analyze large sets of  samples. The DHPLC machine can differentiate which samples are positive for polymorphisms, and these samples only can then be sequenced. This can save investigators a lot of money.

Detection of SNPs with SNP-RFLP

A simple method for detecting SNPs is SNP-restriction fragment length polymorphism (SNP-RFLP). If an allele contains a recognition site for a restriction enzyme while the allele for a SNP does not, digestion of the two alleles will yield two restriction products of different number and length.

Copyright Molecular Station 2012

 

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