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What are SNP

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 letters²C, 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".

SNPs occur normally throughout a person¶s DNA. They occur once in every 300 nucleotides

on average, which means there are roughly 10 million SNPs in the human genome. They can

act as biological markers, helping scientists locate genes that are associated with disease.

When SNPs occur within a gene or in a regulatory region near a gene, they may play a moredirect role in disease by affecting the gene¶s function. 

Types

Single nucleotide  polymorphisms may fall within coding sequences of genes, non-codingregions of genes, or in the intergenic regions between genes. SNPs within a coding sequence

do not necessarily change the amino acid sequence of the protein that is produced, due todegeneracy of the genetic code.

A SNP in which both alleles produce the same polypeptide sequence is called  synonymous  

(sometimes called a silent mutation) ² if a different polypeptide sequence is produced theyare nonsynonymous. A nonsynonymous change may be either  missense, which results in a

different amino acid, or nonsense, which results in a premature stop codon.

SNPs that are not in protein-coding regions may still affect gene splicing, transcription factor  

 binding, or the sequence of non-coding RNA. Gene expression effected by this type of SNP

is referred to as an eSNP (expression SNP) and may be upstream or down stream from thegene.

SNPs may be useful for:y  Determining how an individual will respond to certain drug treatments.

y  Determining if an individual is at risk for developing certain diseases. This includes

consideration of environmental factors, such as the effects of viruses and toxins.

y  Identifying genes associated with complex diseases such as cancer and diabetes.

y  Determining how disease genes are passed from one generation to the next.

y  Assessing the effects of non-genetic factors on health and development, such as diet

and lifestyle.

y  Genetic marking of the genome. SNPs can act as biological markers, allowing moreaccessible navigation of genome maps.

SNPs and Disease DiagnosisEach person's genetic material contains a unique SNP pattern that is made up of many

different genetic variations. Researchers 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

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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 likelyassociated with the disease-causing gene.

SNP and Disease AssociationMany common diseases in humans are not caused by a genetic variation within a single gene

 but are influenced by complex interactions among multiple genes as well as environmental

and lifestyle factors. Although both environmental and lifestyle factors add tremendously to

the uncertainty of developing a disease, it is currently difficult to measure and evaluate their 

overall effect on a disease process. Therefore, we refer here mainly to a person's genetic

predisposition, or the potential of an individual to develop a disease based on genes and

hereditary factors.

Genetic factors may also confer susceptibility or resistance to a disease and determine the

severity or progression of disease. Because we do not yet know all of the factors involved in

these intricate pathways, researchers have found it difficult to develop screening tests for 

most diseases and disorders. By studying stretches of DNA that have been found to harbor a

SNP associated with a disease trait, researchers may begin to reveal relevant genes associated

with a disease. Defining and understanding the role of genetic factors in disease will also

allow researchers to better evaluate the role non-genetic factors  ²such as behavior, diet,

lifestyle, and physical activity²have on disease.