title: Patterns of linkage disequilibrium between SNPs in a Sardinian population isolate and the selection of markers for association studies.
abstract: OBJECTIVE
  In isolated populations, 'background' linkage disequilibrium (LD) has been shown to extend over large genetic distances. This and their reduced environmental and genetic heterogeneity has stimulated interest in their potential for association mapping. We compared LD unit map distances with pair-wise measurements of LD in a dense single nucleotide polymorphism (SNP) set.
  
  
  METHODS
  We genotyped 771 SNPs in an 8 Mb segment of chromosome 22 on 101 individuals from the isolated village of Talana, Sardinia, and compared with outbred European populations.
  
  
  RESULTS
  Heterozygosity was remarkably similar in both populations. In contrast, the extent of LD observed was quite different. The decay of LD with distance is slower in the isolate. The differences in LD map lengths suggest that useful LD extends up to three times farther in the Sardinian population; smaller differences are seen with pairwise LD metrics. While LD map length slightly decreases with average relatedness, cryptic relatedness does not explain the decrease in LD map length. Haplotypes, block boundaries, and patterns of LD are similar in both populations, suggesting a shared distribution of recombination hotspots.
  
  
  CONCLUSIONS
  About 15% fewer haplotype tagging SNPs need to be genotyped in the isolate, and possibly 70% fewer if selecting SNPs evenly spaced on the metric LD map.
authors.affiliation: Shardna Life Sciences, Cagliari, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Angius
authors.forename: Fiona C L
authors.initials: FC
authors.lastname: Hyland
authors.forename: Ivana
authors.initials: I
authors.lastname: Persico
authors.forename: Nicola
authors.initials: N
authors.lastname: Pirastu
authors.forename: Trevor
authors.initials: T
authors.lastname: Woodage
authors.forename: Mario
authors.initials: M
authors.lastname: Pirastu
authors.forename: Francisco M
authors.initials: FM
authors.lastname: De la Vega
mesh_terms: D002892:Chromosomes, Human, Pair 22; D005819:Genetic Markers; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D007558:Italy; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers