title: Evaluating coverage of exons by HapMap SNPs.
abstract: Genome-wide association (GWA) studies are currently one of the most powerful tools in identifying disease-associated genes or variants. In typical GWA studies, single-nucleotide polymorphisms (SNPs) are often used as genetic makers. Therefore, it is critical to estimate the percentage of genetic variations which can be covered by SNPs through linkage disequilibrium (LD). In this study, we use the concept of haplotype blocks to evaluate the coverage of five SNP sets including the HapMap and four commercial arrays, for every exon in the human genome. We show that although some Chips can reach similar coverage as the HapMap, only about 50% of exons are completely covered by haplotype blocks of HapMap SNPs. We suggest further high-resolution genotyping methods are required, to provide adequate genome-wide power for identifying variants.
authors.affiliation: Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Dong
authors.forename: Tingyan
authors.initials: T
authors.lastname: Zhong
authors.forename: Tao
authors.initials: T
authors.lastname: Xu
authors.forename: Yunting
authors.initials: Y
authors.lastname: Xia
authors.forename: Biqing
authors.initials: B
authors.lastname: Li
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.forename: Liyun
authors.initials: L
authors.lastname: Yuan
authors.forename: Guohui
authors.initials: G
authors.lastname: Ding
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
mesh_terms: D005091:Exons; D015894:Genome, Human; D060005:Genotyping Techniques / Q000592:standards; D060148:HapMap Project; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control