HSLS Update

Searching for Single Nucleotide Polymorphisms

Scientists expect that comparison of genomic sequences taken from two unrelated individuals of the same sex will reveal that they are 99.9 percent identical. The 0.1 percent difference is due to genetic variations, mainly from one form of variation called single nucleotide polymorphisms (SNPs).

These polymorphisms are considered one of the key factors that makes each of us different, and can have a major impact on how we respond to diseases, environmental insults such as bacteria, viruses and chemicals, drugs and other therapies. The study of genetic variations is of great value for development of pharmaceutical products and medical diagnostics.

The National Center for Biotechnology Information (NCBI) Single Nucleotide Polymorphism database (dbSNP) is a public-domain archive for a broad collection of simple genetic polymorphisms. This databases of polymorphisms includes:

• Single-base nucleotide substitutions (also known as single nucleotide polymorphisms or SNPs)
• Small-scale multi-base deletions or insertions (also called deletion insertion polymorphisms or DIPs), and
• Microsatellite repeat variations (also called short tandem repeats or STRs).

dbSNP is a part of the Entrez integrated information retrieval system and can be searched using a combination of 28 different search fields. A complete list of search fields can be found on the Entrez SNP site <www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp>.

An Example Illustrating the Step-by-step Retrieval of SNPs:

Mutations on BRCA1 gene have been reported to be associated with the early onset of breast cancer. Retrieve all non-synonymous coding SNPs for human BRCA1. (Non-synonymous coding SNPs create a new codon which codes for a new amino acid.)

1) Go to Entrez SNP Type "BRCA1 [Gene Name]" in the search boxClick on "Limits"

2) Go to "Function Class" and select "coding nonsynonymous" Go to "Organism(s)" and select "Homo Sapiens" Click on "Go" to retrieve results

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3) From this results page, you can retrieve detailed SNP information, and you can visualize SNPs in a genome or gene oriented fashion.

To learn more, visit the HSLS molecular biology and genetics Web portal at <www.hsls.pitt.edu/guides/genetics>.

--Ansuman Chattopadhyay