ASCI 896 Statistical Genomics

Gota Morota
1/14/16

Linkage disequilibrium

Linkage disequilibrium (LD)

  • also known as gametic phase disequilibrium
  • statistical association between alleles at two loci
    • covariance of allelic content at two loci
  • LD map
    • two loci in high LD tend to be physically close to each other
    • LD of two loci decays on average with the distance
  • shares similar concept with pedigree relationships
    • related individuals vs. distantly related individuals

Expected values

  • Expectation of allelic content
    • \( E(x) = p \)
  • Expectation of allelic counts
    • \( E(X) = 2p \)

Variance and Covariance

  • Variance of allelic content
    • \( Var(x) = p(1-p) \)
  • Variance of allelic counts
    • \( Var(X) = 2p(1-p) \)
  • Coariance between allelic content
    • \( Cov(x,y) = D \)
  • Covariance between allelic counts
    • \( Cov(X,Y) = 2D \)