Gota Morota

1/14/16

Linkage disequilibrium

- 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

- Expectation of allelic content
- \( E(x) = p \)

- Expectation of allelic counts
- \( E(X) = 2p \)

- 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
- \( Cov(X,Y) = 2D \)