linkage disequilibrium and lod

Question

Linkage disequilibrium and LOD score

1.       Gene A has two alleles, A₁ and A₂. Gene B has two alleles, B₁ and B₂. In a population, the following haplotype frequencies were observed: A₁B₁ = 0.2, A₂B₂ = 0.45, A₁B₂ = 0.15 and A₂B₁ = 0.2. Calculate the extent of linkage disequilibrium.

2.       Assume the disease genotype is known, as A is the disease allele and a is the normal allele. The marker has four alleles (1, 2, 3,4).

a.       How many meiosis do we see in the pedigree?

b.      How many meiosis are informative for linkage analysis

c.       Calculate the LOD score assuming the genetic distances are 10 and 20 cM.

3.       This pedigree has 5 children. The assumption is the same as in question 2.

 

b.      What is the LOD score at genetic distance 50 cM

c.       What is the maximum LOD score?