title: High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
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.
authors.affiliation: Laboratory of Population Genetics, Division of Cancer Epidemiology and Genetics, and Office of Genomics, National Cancer Institute, Bethesda, MD 20892-5060, USA. buetowk@nih.gov
authors.forename: K H
authors.initials: KH
authors.lastname: Buetow
authors.forename: M
authors.initials: M
authors.lastname: Edmonson
authors.forename: R
authors.initials: R
authors.lastname: MacDonald
authors.forename: R
authors.initials: R
authors.lastname: Clifford
authors.forename: P
authors.initials: P
authors.lastname: Yip
authors.forename: J
authors.initials: J
authors.lastname: Kelley
authors.forename: D P
authors.initials: DP
authors.lastname: Little
authors.forename: R
authors.initials: R
authors.lastname: Strausberg
authors.forename: H
authors.initials: H
authors.lastname: Koester
authors.forename: C R
authors.initials: CR
authors.lastname: Cantor
authors.forename: A
authors.initials: A
authors.lastname: Braun
mesh_terms: D000483:Alleles; D016384:Consensus Sequence; D017931:DNA Primers; D020224:Expressed Sequence Tags; D005240:Feasibility Studies; D005819:Genetic Markers; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010865:Pilot Projects; D017354:Point Mutation; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D017931:DNA Primers; D005819:Genetic Markers