Single nucleotide polymorphism


A variation a single nucleotide at a specific location of the genome that is due to a single base substitution that is present at an appreciable frequency between individuals of a single interbreeding population.

Single-nuucleotide polymorphisms(SNPs) are low risk genetic changes associated with an increased risk of cancer.

A single-nucleotide polymorphism, often abbreviated to SNP

Is a variation in a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population (e.g. > 1%).

SNPs underlie differences in susceptibility to disease.

A wide range of human diseases, e.g. sickle-cell anemia, β-thalassemiaand cystic fibrosis result from SNPs.

The severity of illness and how the body responds to treatments are also manifestations of genetic variations.

A single-base mutation in the APOE (apolipoprotein E) gene is associated with a higher risk for Alzheimer’s disease.

A single-nucleotide variant (SNV) is a variation in a single nucleotide without any limitations of frequency and may arise in somatic cells.

A somatic single-nucleotide variation may also be called a single-nucleotide alteration.

Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions.

SNPs within a coding sequence do not necessarily change the amino acid sequence of the protein that is produced.

Coding region SNPs are of two types: synonymous and nonsynonymous.

Synonymous SNPs do not affect the protein sequence, while nonsynonymous SNPs change the amino acid sequence of protein.

The nonsynonymous SNPs are of two types: missense and nonsense.

SNPs that are not in protein-coding regions may still affect gene splicing, transcription factor binding, messenger RNA degradation, or the sequence of noncoding RNA.

Expression SNP may be upstream or downstream from the gene.

There are millions of known SNP’s occurring in known locations across the entire genome.

The associated SNP’s mark a region of the human genome that influences the risk of disease.

Association studies help to determine whether a genetic variant is associated with a disease or trait.

A tag SNP is a representative single-nucleotide polymorphism (SNP’s) in a region of the genome with high linkage disequilibrium, which is the non-random association of alleles at two or more loci.

Sets of alleles or DNA sequences can be clustered so that a single SNP can identify many linked SNPs.

Occur in non-coding regions more frequently than in coding regions or, in general, where natural selection is acting and eliminating other variants of the SNP that constitutes the most favorable genetic adaptation.

Genetic recombination and mutation rate, can also determine SNP density.

SNP density can be predicted by the presence of microsatellites.

There are variations between populations, so a SNP allele that is common in one geographical or ethnic group may be much rarer in another.

Variations in the DNA sequences affects how diseases develop and respond to pathogens, chemicals, drugs, vaccines, and other agents.

SNPs may be used in forensics for some phenotypic clues like eye color, hair color and ethnicity

Some SNPs are associated with the metabolism of different drugs.

A single SNP may cause a Mendelian disease.

For complex diseases, SNPs do not usually function individually, rather, they work in coordination with other SNPs to manifest a disease condition as has been seen in osteoporosis.

All types of SNPs can have an observable phenotype or can result in disease.

SNPs in non-coding regions can manifest in a higher risk of cancer, and may affect mRNA structure and disease susceptibility.

Non-coding SNPs can also alter the level of expression of a gene.

Substitutions of SNPs in coding regions do not result in a change of amino acid in the protein, but still can affect its function.

Nonsynonymous substitutions:

missense – single change in the base results in change in amino acid of protein and its malfunction which leads to disease.

nonsense – point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codonin the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product.

Methods to discover SNPs include:

DNA sequencing;

capillary electrophoresis;

mass spectrometry;

single-strand conformation polymorphism (SSCP);

single-base extension;

electrochemical analysis;

denaturating HPLC and gel electrophoresis;

restriction fragment length polymorphism;

hybridization analysis;

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