8/24/2015 Making SNPs Make Sense

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HOME PHARMACOGENOMICS MAKING SNPS MAKE SENSE

Scientists are identifying, cataloging, and studying small geneticvariations among humans that will lead to more specialized andeffective medical treatments. What do these variations look like, andwhat exactly makes them informative?

Researchers look for one or more single nucleotide polymorphisms(SNPs; pronounced "snips"). SNPs are single-nucleotide substitutionsof one base for another that occur in more than one percent of thegeneral population.

The challenge for scientists is to identify SNPs that correlate with aparticular effect in patients. Reliable SNPs could serve as predictivemarkers that inform our decisions about numerous aspects ofmedical care, including specific diseases, effectiveness of variousdrugs and adverse reactions to specific drugs.

This pharmacogenetic approach could save time, money, anddiscomfort for millions of patients through accurate diagnoses andmatching patients with appropriate medicines.

Scientists approach the problem of identifying, cataloging, and characterizingSNPs in two main ways:

Genomic approaches. This approach is used by scientists who want to seethe big picture. Several large-scale projects have combined the efforts ofmany institutions to identify and catalog all of the SNPs in the 3-billion-basepair human genome. Each project involves hundreds of scientists, whocompare the genomes of numerous individuals to identify the differences.These comparisons require a lot of computer-powered data analysis. As theywork, scientists sort and catalog their results in databases that are availableto anyone over the Internet, including other scientists and you.

Functional approaches. This approach is used by scientists who areinterested in a particular disease or drug response. The biological processesinvolved in diseases and drug responses are controlled by the activities ofmany genes. Scientists interested in a particular process select genes knownto be involved in the process and examine them in people who have aresponse or disease, as well as those who don't. By comparing people's DNAsequences, scientists can identify SNPs that correspond with a particularfunction or response.

Making SNPs Make Sense

Finding SNPs in the human genome

8/24/2015 Making SNPs Make Sense

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SNP (pronounced "snip") stands for Single Nucleotide Polymorphism. SNPs aresingle-nucleotide substitutions of one base for another. Each SNP location in thegenome can have up to four versions: one for each nucleotide, A, C, G, and T. ASNP and its distribution in a population might look like the images below and tothe left.

Not all single-nucleotide changes are SNPs, though. To be classified as a SNP,two or more versions of a sequence must each be present in at least onepercent of the general population.

SNPs occur throughout the human genome—about one in every 300 nucleotidebase pairs. This translates to about 10 million SNPs within the 3-billion-nucleotide human genome.

SNP Quick Reference

SNPs and disease-causing mutations: Not the same!

8/24/2015 Making SNPs Make Sense

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If you know what a point mutation is, then the description of a SNP might soundsimilar. True, both are single-nucleotide differences in a DNA sequence, butSNPs should not be confused with disease-causing mutations. The image to theleft shows some tell-tale differences:

First, to be classified as a SNP, the change must be present in at least onepercent of the general population. No known disease-causing mutation is thiscommon.

Second, most disease-causing mutations occur within a gene's coding orregulatory regions and affect the function of the protein encoded by the gene.Unlike mutations, SNPs are not necessarily located within genes, and they donot always affect the way a protein functions. SNPs are divided into two maincategories:

Linked SNPs (also called indicative SNPs) do not reside within genes and donot affect protein function. Nevertheless, they do correspond to a particulardrug response or to the risk for getting a certain disease.

Causative SNPs affect the way a protein functions, correlating with adisease or influencing a person's response to medication. Causative SNPscome in two forms:

Coding SNPs, located within the coding region of a gene, change theamino acid sequence of the gene's protein product.

Non-coding SNPs, located within the gene's regulatory sequences,change the timing, location, or level of gene expression.

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