3. Linkage disequilibrium (LD) occurs when alleles at different loci are nonrand

Question

3. Linkage disequilibrium (LD) occurs when alleles at different loci are nonrandomly associated and are more likely to be inherited together. But how do scientists identify LD? For this question, you will calculate D, the coefficient of linkage disequilibrium to test whether a set of SNPs is in linkage equilibrium or disequilibrium.

Suppose there are two variable sites (SNPs) on two different loci, and we collect sequence data from a sample of 2000 people. At SNP1, the nucleotide in the locus sequence is either a G or a C, while at SNP2, the nucleotide is either an A or a T. All combinations of SNP1 and SNP2 nucleotides are possible, and from the data we see that there are 474 individuals with GA haplotype, 611 with a GT haplotype, 142 with a CA haplotype, and 773 individuals with CT haplotype.

a) What are the haplotype frequencies? Show work below:

b) Now, let’s calculate D. D = (g11 x g22) - (g12 x g21). Show work below. Are these loci in LD?
g11 = frequency of GA
g12 = frequency of GT
g21 = frequency of CA
g22 = frequency of CT

Explanation / Answer

Answer :

Frequency of GA=g11= 474/2000=0.237

Frequency of GT= 611/2000=0.3055

Frequency of CA= 142/2000=0.071

Frequency of CT= 773/2000= 0.3865

So D= (G11-g22)-(g12-g21)=(0.237*0.3865)-(0.3055*0.071)

= 0.916005-0.0216905=0.916--0.0217=0.8943=0.9(approx)

So these are loci of LD

Related Questions

Navigate

• Browse (All)
• Browse 3
• Subjects

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.