title: Fine-scale structure of the genome and markers used in association mapping.
abstract: 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.
authors.affiliation: Genetic Epidemiology Division, Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Curtin
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Camp
mesh_terms: D056726:Genetic Association Studies / Q000379:methods*; D005819:Genetic Markers; D015894:Genome, Human / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D009154:Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011995:Recombination, Genetic
chemical_list: D005819:Genetic Markers