Snp Genotyping Single Nucleotide Polymorphisms

Our characteristics as human beings, such as hair color and height, are decided by our six billion base pairs of DNA. While most human DNA is identical, about 3 million pairs (one twentieth of a percent) vary from person to person. These variations not only give us our physical characteristics, but they also make us predisposed to certain genetic diseases.

Genomes, the complete genetic sequence on one set of chromosomes, are composed of four nucleotides: adenine (A); cytosine (C); thymine (T); and guanine (G). Single nucleotide polymorphisms, or SNPs (pronounced “snips”) occur when a single nucleotide in the genome sequence is changed. Nearly 70 percent of SNPs involve replacing cytosine with thymine (example: AAGGCTAA to AAGGTTAA). The variation must take place in at least one percent of the population to be considered a SNP.

These DNA variations can have a key impact on how people respond to disease, bacteria, viruses, toxins, chemicals and drugs. For this reason, SNPs are helpful in developing pharmaceutical products or medical diagnostics, and for biomedical research. Since SNPs don’t change much through generations, they are easy to track in population studies.

Identifying Disease Potential

SNPs don’t actually cause illnesses, but they can be studied to determine an individual’s predisposition for contracting a particular disease. For example, the gene apolipoprotein E (ApoE) is associated with Alzheimer’s disease. Three possible alleles exist for ApoE – E2, E3 and E4 – due to the two SNPs that exist on the gene.

Human beings inherit one copy of ApoE from both of their parents. Statistics have shown that an individual who inherits at least one E4 allele is more likely to develop Alzheimer’s disease. Similarly, the inheritance of an E2 allele means the person is less likely to develop the disease.

Of course, this is not an exact science. Many individuals with two E4 alleles never develop Alzheimer’s – and two E2 alleles won’t rule out Alzheimer’s completely. Plus, ApoE is only one of many genes that contribute to this particular disease, which makes it hard to predict using only SNP genotyping.

Diseases That Can Be Identified by SNP Genotyping

Risks for many genetic diseases can be identified by SNP testing DNA. These include:

  • alcoholism
  • Alzheimer’s disease
  • arthritis
  • asthma
  • cancer
  • depression
  • diabetes
  • heart disease
  • Parkinson’s disease.

Issues Related to SNP Testing DNA

SNP testing is viewed with trepidation by some scientists for a variety of reasons. First, many diseases involve the interaction of several genes and the environment, so it can be difficult to predict if an individual will contract the disease using only SNP testing.

Also, some doctors worry that the knowledge that an individual is prone to a certain disease may drive the individual to depression or even suicide. They believe that some people aren’t able to cope with the knowledge that they are genetically inclined to contract specific diseases, particularly ones that are necessarily fatal.

Practical Uses for SNPs

SNP genotyping contributes to a more in-depth understanding of the human genome, and it allows scientists a better understanding of the hereditary nature of certain diseases. Studying SNPs can also help predict how an individual will respond to a certain drug, making this type of testing useful to the pharmaceutical industry.

SNP genotyping can also be used in agriculture, animals, plants and fisheries for reproduction and selection of desired traits.

Resources

Genetic Engineering and Biotechnology News. (2006). SNP genotyping methods surge ahead. Retrieved September 9, 2008, from the Genetic Engineering and Biotechnology News Web site: http://www.genengnews.com/articles/chitem.aspx?aid=1760&chid=2

Human Genome Project Information. (2008). SNP fact sheet. Retrieved September 9, 2008, from the Human Genome Project Web site: http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml

National Human Genome Research Institute. (n.d.). Genetic variation program. Retrieved September 9, 2008, from the NHGRI Web site: http://www.genome.gov/page.cfm?pageID=10001551

Nova Teachers. (2008). NOVAscienceNOW: Personal DNA testing. Retrieved September 9, 2008, from the PBS Web site: http://www.pbs.org/wgbh/nova/teachers/programs/0302_01_nsn.html

Science Advisory Board. (n.d.). SNP genotyping technology. Retrieved September 9, 2008, from the Science Advisory Board Web site: http://www.scienceboard.net/studies/studies.asp?studyId=62