single nucleotide polymorphism (snps)
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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/
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