Midterm 1 - Notes 4 (Part 2)

Question 1

What is the most common severe musculoskeletal birth defect?

Answer 1

Club foot disease

Question 2

Club foot disease

Answer 2

Is a disease (normally presented at birth) that has the foot pointing down and inwards and the soles of the feet are facing each other

Question 3

What are the odds of a child getting club foot?

Answer 3

1 in 1,000

Question 4

What kind of component does clubfoot have?

Answer 4

A genetic component

• 25% of cases are familia
• inherited throughout generations

Question 5

What kind of condition is club foot disease?

Answer 5

Clubfoot segregates as an autosomal dominant condition

Question 6

What does an autosomal dominant condition mean?

Answer 6

It means you only need one mutation to cause the disease (instead of 2)

Question 7

What is LOD?

Answer 7

It is the probability of linkage over the probability of no linkage

Question 8

What does it mean when the Max LOD score of the club foot disease was 3.31?

Answer 8

Since it is over 3 that means it is 1000x more likely that there is a linkage

Question 9

What can they conclude from the 3.31 LOD score?

Answer 9

That there might be multiple locations that contribute to the disease, but there is a region that effects more common

Question 10

What probably doesnt happen in the club foot study because of the small sample size?

Answer 10

Co-segregation

Question 11

Pitx1

Answer 11

Is a transcription master regulator

- important in hind limb development

Question 12

What is the benefit of having so many markers?

Answer 12

We are able to actually trace the break points of the haplotype blocks

Question 13

In the club foot study what was the SNP allele found in all healthy individuals?

Answer 13

The G allele

Question 14

In the club foot study what was the SNP allele found in all affected individuals?

Answer 14

The A allele

Question 15

Where were the SNPs located?

Answer 15

On the coding region

- nonsynonymous

Question 16

What did Glu change to?

Answer 16

Lys (E130K)

Question 17

Pitx1 protein

Answer 17

is a transcription factor that binds to the cis regulatory element and have other target genes regulating the activation of transcription

Question 18

Why did they expand there sample range to 500 healthy humans in the club foot study?

Answer 18

To see if the SNP was present in those individuals who did not have a club foot
- that way we can tell if this change is a potential cause for the club foot

Question 19

Were is the Pitx1 gene located?

Answer 19

In the DNA binding domain

- homeodomain

Question 20

Homeodomain

Answer 20

Is a special class of helix-turn-helix DNA binding domain 
- helices 2 and 3 make this up

Question 21

Is Glu high conserved among Pitx1 families?

Answer 21

Yes

Question 22

What did the mutations replace Glu acidic amino acid with?

Answer 22

A basic one –> Lys, K

Question 23

What could happen if you change the charge from positive to negative?

Answer 23

It could effect the interaction of the targets

Question 24

What does the cross section perform?

Answer 24

Immediate DNA interaction in the transcriptional genes

Question 25

What was the hypothesis of the Glu to Ly(E130K) mutation?

Answer 25

E130K mutation affects DNA binding specificity of Pitx1

• affects transcriptional activation of target genes
• -> affects normal leg development
• this is what causes the disease phenotype

Question 26

What happens if you reduce binding to core binding site in the Pitx1 E130K mutant?

Answer 26

It reduces the activation of targets in E130K Pitx1

Question 27

What is the result when Pitx1 is KO of mice? (3)

Answer 27

1. Lethal
2. Reduces hind limbs
3. Loss of all function

Question 28

What is the result when cis-element is deleted? (2)

Answer 28

1. Loss of expression only in pelvis
   - coding region was fine
2. Pelvic spine reduction

Question 29

What is the result when there is a point mutation in the homeodomain? (2)

Answer 29

1. Reduced protein (TF) activity
2. Hind limb malfunctions
   - still works but not as efficient as the wild type