Fine-Scale Structure of the Genome and Markers Used in Association Mapping

  • Karen Curtin
  • Nicola J. Camp
Part of the Methods in Molecular Biology book series (MIMB, volume 713)


In this chapter, mutation (specifically single-nucleotide polymorphisms, SNPs) and recombination will be covered in more detail, and the concepts of genotype and haplotype will be reviewed. Linkage disequilibrium (LD) describes the strength of a relationship between alleles at different loci. The definition for LD, its visual representation, and the calculation of statistics that measure LD will be presented. The power of genetic association studies to identify disease susceptibility alleles fundamentally relies on the genetic variants studied. A standard approach is to determine a set of tagging-SNPs (tSNPs) that capture the majority of genomic variation in regions of interest by exploiting local correlation structures. The concept of LD and how it is used to select tSNPs will be addressed, as well as specific procedures and algorithms that are practiced by researchers to determine these variants.

Key words

Linkage disequilibrium Haplotype blocks Mutation Recombination Tagging-SNPs 


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Karen Curtin
    • 1
  • Nicola J. Camp
    • 1
  1. 1.Genetic Epidemiology Division, Department of Biomedical InformaticsUniversity of UtahSalt Lake CityUSA

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