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High-throughput development and characterization of a genomewide collection of gene-based single nucleotide
K H Buetow1, M Edmonson, R MacDonald
1Laboratory of Population Genetics, Division of Cancer Epidemiology and Genetics, and Office of Genomics, National Cancer Institute, Bethesda, MD 20892-5060, USA. buetowk@nih.gov
Abstract:
We describe here a system for the rapid identification, assay development, and characterization of gene-based single nucleotide polymorphisms (SNPs). This system couples informatics tools that mine candidate SNPs from public expressed sequence tag resources and automatically designs assay reagents with detection by a chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry platform. As a proof of concept of this system, a genomewide collection of reagents for 9,115 gene-based SNP genetic markers was rapidly developed and validated. These data provide preliminary insights into patterns of polymorphism in a genomewide collection of gene-based polymorphisms.