Editor of this issue:

William Self, Medical Library Center of New York, 7 East 102nd St., 7th Floor, New York, NY 10029, S-1, Phone: 212-427-1630, Fax: 212-860-3496, E-mail: wself@mlcny.org.

The single nucleotide polymorphism (SNP) [pronounced "snip"] is the most common form of genetic variation. As the name suggests, each SNP is a difference in a single nucleotide (A,T,C,or G) of an individual's DNA sequence, such as having AAGG instead of ATGG. There may be from 1 to 10 million SNPs in the entire human genome, but perhaps only a few thousand relate to disease outcomes. The numbers seem to change with every news report.

SNP patterns from a target population can be compared with SNP patterns from unaffected populations to find genetic variations shared only by the affected group.

The most useful SNPs are known as "functional SNPs." A single functional SNP or certain combinations of functional SNPs may help explain variability in individual responses to a given drug or pinpoint the subtle genetic differences that predispose some to diseases such as arthritis, Alzheimer's, cancer, diabetes, and depression.

Identifying and mapping SNPs on the human genome is fundamental to molecular medicine. There are many advanced technologies to detect SNPs. One of these technologies, the microarray, will be covered in a future column. SNPs act as genetic markers and can be associated with genes on maps. The SNP Consortium of pharmaceutical companies, national organizations and universities are working together to create a large, high-density and high-quality SNP map to be in the public domain for use in studies of SNP patterns. See the graphics "How will a SNP Map Be Used? Identification of susceptibility genes" and "Pharmacogenetics" from SNPs - Genetic Research @ GlaxoSmithKline [http://genetics.glaxowellcome.com/genomics.asp#snps] for a visual interpretation.

Resources

• Listen to a detailed explanation of SNPs from Dr. Francis Collins, director of the National Human Genome Research Institute http://www.nhgri.nih.gov/RealMediaMetaFiles/DIR/OSE/Audio/snps.ram



• SNP Fact Sheet - Human Genome Project Information
  The two Nature articles listed are great background reading. http://www.ornl.gov/hgmis/faq/snps.html



• A brief guide to SNPs - The Wellcome Trust
  http://www.wellcome.ac.uk/en/1/biovensnpblf.html



• dbSNP [a searchable database of SNPs] - National Center for Biotechnology Information
  http://www.ncbi.nlm.nih.gov/SNP/