Lecture 9/28 - E2

Question 1

What does allelic phase mean?

Answer 1

Knowing which specific alleles are next to one another on the same chromosome

Question 2

What is a LOD score used for?

Answer 2

To test the likelihood that two loci are linked vs the likelihood that they are unlinked.

Question 3

How is a LOD score calculated?

Answer 3

LOD = log (likelihood if linked) / (likelihood if unlinked)

Question 4

How do you interpret the LOD score?

Answer 4

The greater the LOD score, the more likely the genes are linked

Question 5

A LOD score of 3+ is considered…

Answer 5

In favor of linkage

Question 6

LOD scores of less than -2 are considered…

Answer 6

In favor of unlinkage

Question 7

LOD scores between -2 and +3 are considered…

Answer 7

Inconclusive

Question 8

How do you relate the Z max value and Theta max value when given a table of the LOD scores at different recombination values?

Answer 8

First, find the largest number which should be close to Zmax.
Then, look at Theta max to find the distance.
Example 0.13 Theta = 13 map units away

Question 9

What is a haplotype?

Answer 9

The full arangement of alleles on each homolog is called the individuals haplotype

Question 10

What is linkage equilibrium?

Answer 10

The likelihood of a particular haplotype is the product of the individual allele frequencies in the population.

Question 11

For instance, for genes A and B, let’s say that there are two A alleles, A1 and A2, where A1 is found inthe population at 20% and A2 is found at 80%. B1 is found at 30% and B2 is found at 70%. Under the conditions of linkage equilibrium, the likelihood of finding specific haplotypes are:

Answer 11

A1B1 = 0.2 x 0.3 = 0.06
A1B2 = 0.2 x 0.7 = 0.14
A2B1 = 0.8 x 0.3 = 0.24
A2B2 = 0.8 x 0.7 = 0.56
All total to 1.00

Question 12

When halplotype frequencies deviate significantly from what is expected (product of each occurance), this is called…

Answer 12

Linkage Disequilibrium

Question 13

When does linkage disequilibrium occur?

Answer 13

Usually when the genes in question are physically very close together (tightly linked)

Question 14

What are Single Nucleotide Polymorphisms (SNPs) and what are some of their characteristics?

Answer 14

Base pair differences in the same gene
They are present in everyon’e DNA
Some can play a causative role in disease by affecting the gene’s function
They are mainly used at DNA landmarks helping scietists located genes related to genetic disorders