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Single Nucleotide Polymorphism(SNPs)

Name:SB Mirza; 1st smester; MS Bioinformatics Submitted to:Dr Qaiser Fatimi

10/3/2011

Comsats institute of information technology

Single Nucleotide Polymorphism:

A Single Nucleotide Polymorphism, or SNP (pronounced "snip"), is a small genetic change, or

variation, that can occur within a person's DNA sequence. The genetic code is specified by the

four nucleotide "letters" A (adenine), C (cytosine), T (thymine), and G (guanine). SNP variation

occurs when a single nucleotide, such as an A, replaces one of the other three nucleotide

letters—C, G, or T.

An example of a SNP is the alteration of the DNA segment AAGGTTA to ATGGTTA, where

the second "A" in the first snippet is replaced with a "T". On average, SNPs occur in the human

population more than 1 percent of the time. Because only about 3 to 5 percent of a person's DNA

sequence codes for the production of proteins, most SNPs are found outside of "coding

sequences". SNPs found within a coding sequence are of particular interest to researchers

because they are more likely to alter the biological function of a protein. Because of the recent

advances in technology, coupled with the unique ability of these genetic variations to facilitate

gene identification, there has been a recent flurry of SNP discovery and detection.

SNPs and Disease Diagnosis:

Each person's genetic material contains a

unique SNP pattern that is made up of many

different genetic variations. Resear chers

have found that most SNPs are not

responsible for a disease state. Instead, they

serve as biological markers for pinpointing a

disease on the human genome map, because

they are usually located near a gene found to

be associated with a certain disease.

Occasionally, a SNP may actually cause a

disease and, therefore, can be used to search

for and isolate the disease-causing gene.

To create a genetic test that will screen for a

disease in which the disease-causing gene has

already been identified, scientists collect

blood samples from a group of individuals

affected by the disease and analyze their

DNA for SNP patterns. Next, researchers

compare these patterns to patterns obtained

by analyzing the DNA from a group of

individuals unaffected by the disease. This

type of comparison, called an "association

study", can detect differences between the

SNP patterns of the two groups, thereby indicating which pattern is most likely associated with

the disease-causing gene. Eventually, SNP profiles that are characteristic of a variety of diseases

will be established. Then, it will only be a matter of time before physicians can screen

individuals for susceptibility to a disease just by analyzing their DNA samples for specific SNP

patterns. It will only be a matter of time before physicians can screen patients for susceptibility

to a disease by analyzing their DNA for specific SNP profiles.

SNPs and Drug Development:

As mentioned earlier, SNPs may also be associated with the absorbance and clearance of

therapeutic agents. Currently, there is no simple way to determine how a patient will respond to a

particular medication. A treatment proven effective in one patient may be ineffective in others.

Worse yet, some patients may experience an adverse immunologic reaction to a particular drug.

Today, pharmaceutical companies are limited to developing agents to which the "average"

patient will respond. As a result, many drugs that might benefit a small number of patients never

make it to market.

In the future, the most appropriate drug for an individual could be determined in advance of

treatment by analyzing a patient's SNP profile. The ability to target a drug to those individuals

most likely to benefit, referred to as "personalized medicine", would allow pharmaceutical

companies to bring many more drugs to market and allow doctors to prescribe individualized

therapies specific to a patient's needs.

The SNP effort will serve as the bedrock of pharmacogenomics, the emerging field of

personalized medicine: the right drug, in the right dose, to the right person, at the right time

Types of SNPs:

SNPs should not be confused with disease-causing mutations.

The image to the left shows some tell-tale differences:

First, to be classified as a SNP, the change must be present in

at least one percent of the general population. No known

disease-causing mutation is this common.

Second, most disease-causing mutations occur within a gene's

coding or regulatory regions and affect the function of the

protein encoded by the gene. Unlike mutations, SNPs are not

necessarily located within genes, and they do not always

affect the way a protein functions. SNPs are divided into two

main categories:

Linked SNPs (also called indicative SNPs) do not reside

within genes and do not affect protein function. Nevertheless,

they do correspond to a particular drug response or to the risk for getting a certain disease.

Causative SNPs ,affect the way a protein functions, correlating with a disease or influencing a

person's response to medication. Causative SNPs come in two forms:

Coding SNPs, located within the coding region of a gene, change the amino acid sequence of the

gene's protein product.

Non-coding SNPs, located within the gene's regulatory sequences, change the level of gene

expression and, therefore, how much RNA and protein is produced.

Use and importance:

Variations in the DNA sequences of humans can affect how humans develop diseases and

respond to pathogens, chemicals, drugs, vaccines, and other agents. SNPs are also thought to be

key enablers in realizing the concept of personalized medicine.[2]

However, their greatest

importance in biomedical research is for comparing regions of the genome between cohorts

(such as with matched cohorts with and without a disease) in genome-wide association studies.

The study of SNPs is also important in crop and livestock breeding programs.They are usually

biallelic and thus easily assayed. 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.

Refrences:

1. https://www.23andme.com/gen101/snps/

2. http://learn.genetics.utah.edu/content/health/pharma/snips/

3. http://www.ncbi.nlm.nih.gov/About/primer/snps.html

4. http://ghr.nlm.nih.gov/handbook/genomicresearch/snp

5. http://www.ncbi.nlm.nih.gov/projects/SNP/