title: SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
abstract: BACKGROUND
  During this recent decade, microarray-based single nucleotide polymorphism (SNP) data are becoming more widely used as markers for linkage analysis in the identification of loci for disease-associated genes. Although microarray-based SNP analyses have markedly reduced genotyping time and cost compared with microsatellite-based analyses, applying these enormous data to linkage analysis programs is a time-consuming step, thus, necessitating a high-throughput platform.
  
  
  RESULTS
  We have developed SNP HiTLink (SNP High Throughput Linkage analysis system). In this system, SNP chip data of the Affymetrix Mapping 100 k/500 k array set and Genome-Wide Human SNP array 5.0/6.0 can be directly imported and passed to parametric or model-free linkage analysis programs; MLINK, Superlink, Merlin and Allegro. Various marker-selecting functions are implemented to avoid the effect of typing-error data, markers in linkage equilibrium or to select informative data.
  
  
  CONCLUSIONS
  The results using the 100 k SNP dataset were comparable or even superior to those obtained from analyses using microsatellite markers in terms of LOD scores obtained. General personal computers are sufficient to execute the process, as runtime for whole-genome analysis was less than a few hours. This system can be widely applied to linkage analysis using microarray-based SNP data and with which one can expect high-throughput and reliable linkage analysis.
authors.affiliation: Department of Neurology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan. yokofukuda-tky@umin.ac.jp
authors.forename: Yoko
authors.initials: Y
authors.lastname: Fukuda
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Nakahara
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Date
authors.forename: Yuji
authors.initials: Y
authors.lastname: Takahashi
authors.forename: Jun
authors.initials: J
authors.lastname: Goto
authors.forename: Akinori
authors.initials: A
authors.lastname: Miyashita
authors.forename: Ryozo
authors.initials: R
authors.lastname: Kuwano
authors.forename: Hiroki
authors.initials: H
authors.lastname: Adachi
authors.forename: Eiji
authors.initials: E
authors.lastname: Nakamura
authors.forename: Shoji
authors.initials: S
authors.lastname: Tsuji
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008040:Genetic Linkage; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide