title: Evaluation of an algorithm of tagging SNPs selection by linkage disequilibrium.
abstract: BACKGROUND
  Single nucleotide polymorphisms (SNPs) are the most abundant kind of genetic polymorphism in the human genome. They are important in both genetic research and genetic testing in a clinical setting, such as in the area of pharmacogenetics. In order to improve efficiency, tagging SNPs (tagSNPs) are selected in genes of interest to represent other co-related SNPs in linkage disequilibrium (LD) with the tagSNPs. Various algorithms have been proposed to identify a subset of single nucleotide polymorphisms as tagSNPs. Most algorithms of tagSNPs selection are haplotype-based, in which the spatial relationship between SNPs is considered. Currently, a more efficient cluster-based algorithm is proposed which clusters SNPs solely by a LD parameter, such as r(2). Here, we evaluated the sample distribution of r(2) and its effect on the cluster-based tagSNPs selection.
  
  
  METHODS
  The genotype data of 198 individual within a 500-kb region on 5q31 was used to evaluate the sample distribution of r(2) and its effect on the cluster-based tagSNPs selection.
  
  
  RESULTS
  It was found that the degree of variation of LD depends on the LD structure of genes.
  
  
  CONCLUSIONS
  As a cluster-based tagSNPs selection algorithm does not take into account the spatial position of SNPs, a more stringent r(2) threshold is required to achieve more reliable tagSNPs selection.
authors.affiliation: Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong. nelsontang@cuhk.edu.hk
authors.forename: Nelson L S
authors.initials: NL
authors.lastname: Tang
authors.forename: Paul D P
authors.initials: PD
authors.lastname: Pharoah
authors.forename: Suk Ling
authors.initials: SL
authors.lastname: Ma
authors.forename: Douglas F
authors.initials: DF
authors.lastname: Easton
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D030541:Databases, Genetic; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*