Large-Scale Validation of Single Nucleotide Polymorphisms in Gene Regions

Abstract

Genome-wide association studies using large numbers of bi-allelic single nucleotide polymorphisms (SNPs) have been proposed as a potentially powerful method for identifying genes involved in common diseases. To assemble a SNP collection appropriate for large-scale association, we designed assays for 226,099 publicly available SNPs located primarily within known and predicted gene regions. Allele frequencies were estimated in a sample of 92 CEPH Caucasians using chip-based MALDI-TOF mass spectrometry with pooled DNA. Of the 204,200 designed assays that were functional, 125,799 SNPs were determined to be polymorphic (minor allele frequency >0.02), of which 101,729 map uniquely to the human genome. Many of the commonly available RefSNP annotations were predictive of polymorphic status and could be used to improve the selection of SNPs from the public domain for genetic research. The set of uniquely mapping, polymorphic SNPs is located within 10 kb of 66% of known and predicted genes annotated in LocusLink, which could prove useful for large-scale disease association studies.[Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: E. Lai, and O. Osamu.]Single nucleotide polymorphisms (SNPs) are the most abundant genetic variations in the human genome. They occur, on average, once every 300 base pairs of sequence with a minor allele frequency (MAF) greater than 1% (Kruglyak and Nickerson 2001;Stephens et al. 2001;Reich et al. 2003). The high abundance of SNPs and the availability of increasingly high-throughput and cost effective methods of measuring them encourage their use in many kinds of human genetic studies (Marnellos 2003). SNPs are of particular value in whole-genome association studies for identifying the genes involved in complex trait variation (Lander 1996;Risch and Merikangas 1996). The expected number of SNPs required for successful population-based association studies depends on the distribution of linkage disequilibrium (LD) across the genome in the populations of interest. The lengths of genomic segments in strong LD varies tremendously throughout the genome, ranging from less than 1 kilobase pairs (kb) to over 500 kb, with most blocks estimated to be less than 20 kb in Caucasian populations (Daly et al. 2001;Reich et al. 2001;Dawson et al. 2002;Gabriel et al. 2002;Clark et al. 2003). The international haplotype mapping (HapMap) project was initiated to characterize the patterns of LD throughout the human genome to help identify the most informative set of SNP markers for LD mapping (Gibbs et al. 2003).To explore the potential of large-scale association studies, we set out to develop a suitable collection of approximately 100,000 SNPs. With the HapMap project far from completion, the SNPs could not be selected on the basis of LD patterns. Since a collection of 100,000 SNPs would be far too few to provide dense coverage throughout the genome, we primarily focused on SNPs located with...

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