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United States Department of Agriculture

Agricultural Research Service

Title: A web-based genome browser for 'SNP-aware' assay design

item Morris, Joseph
item Heaton, Michael - Mike
item Kalbfleisch, Theodore

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/2/2008
Publication Date: 1/1/2009
Citation: Morris, J.P., Heaton, M.P., Kalbfleisch, T.S. 2009. A web-based genome browser for 'SNP-aware' assay design [abstract]. Plant and Animal Genomes XVII Conference. Abstract No. CP843. Available:

Interpretive Summary:

Technical Abstract: Human and animal genomes contain an abundance of single nucleotide polymorphisms (SNPs) that are useful for genetic testing. However, the relatively large number of SNPs present in diverse populations can pose serious problems when designing assays. It is important to “mask” some SNP positions so assay design algorithms do not allow oligonucleotide primers over these sites, as this may result in allelic dropout. For example, NCBI currently reports 10.6 M and 1.68 M SNPs mapped to the human and bovine genomes, respectively. Not all of these SNPs are polymorphic in populations of interest. To address these and other assay design issues, a web service-based system was developed with a web-based user interface that makes it possible for a research to quickly assess the location and minor allele frequency for SNPs in their population of interest, and make an informed decision as to whether or not the SNP should be masked for the assay design process. The web service application programming interfaces provided with this system make it possible to automate this process for high-throughput assay design, implementing logic that will determine which SNPs need to be masked in a particular population.

Last Modified: 10/19/2017
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