Lecture 9 - Clinical Genetics of Cystic Fibrosis

Question 1

Incidence of CF

Answer 1

~1/2500 - 3000 live births

Question 2

Carrier frequency of CF

Answer 2

~1/25 in northern Europe

Question 3

How strong is the genotype-phenotype correlation in CF?

Answer 3

Strong in some areas (pancreatic insufficiency)

Less strong in other areas (lung blockage)

Question 4

Which mutation classes correlate with pancreatic insufficiency?

Answer 4

Class I, II and III

Question 5

Which mutation classes correlate with more severe lung disease?

Answer 5

Classes I, II and III

Question 6

Which mutation classes correlate with less severe lung disease and pancreatic sufficiency?

Answer 6

Classes IV and V

Question 7

Example of a mutation in CFTR with reduced penetrance

Answer 7

R117H

Question 8

What determines R117H penetrance?

Answer 8

A poly-T tract (5, 7 or 9 T’s) exists on same intron (intron 8) as R117H.
Establishes which mutations are in phase, in cis

5 T’s means R117H will likely cause disease
7 T’s means R117H is unlikely to cause disease
9 T’s means R117H is highly unlikely to cause disease

Question 9

Why might being heterozygous for CF be advantageous for cholera infection?

Answer 9

If 50% of CFTR channels have impaired function, less water might be lost into the gut lumen

Question 10

Why might being heterozygous for CF be advantageous for S. typhi infection?

Answer 10

S. typhi can bind to CFTR.

If 50% of CFTR proteins are misshapen, might reduce bacterial adherence

Question 11

How can environmental vs genetic modifiers be studied for CF?

Answer 11

Compare disease for monozygotic, dizygotic twins, and siblings

Question 12

How genetically-determined is lung function in CF?

Answer 12

50% genetic, 50% environmental

Question 13

How genetically-determined is meconium ileus in CF?

Answer 13

Completely genetically determined

Question 14

How genetically-determined is diabetes in CF?

Answer 14

Mostly genetic

Question 15

Why identify genetic modifiers of CF?
1)
2)
3)
4)

Answer 15

1) New targets for therapies
2) Better understand disease variability
3) Expect mutations to be minimally-penetrant in normal people, but effects unmasked in CF
4) Mutations might have modifying effects on other diseases

Question 16

Do many de novo mutations cause CF?

Answer 16

No

Few de novo mutations leading to CF

Question 17

Ways to identify genetic modifiers of CF
1)
2)
3)

Answer 17

1) Linkage studies
2) Candidate gene association
3) Genome-wide association studies

Question 18

Linkage studies

Answer 18

Track genes or markers associated with a specific phenotype in individuals or families with CF

Question 19

Candidate gene association

Answer 19

Look at genes with a known function (which correlates with CF symptoms)
Correlate variations in gene with different CF phenotypes

Question 20

Genome-wide association studies

Answer 20

Look at DNA markers across whole genome in people with CF and without CF

Look for SNPs which are prevalent more in affected populations than unaffected populations

Question 21

Drawbacks of genome-wide association studies
1)
2)
3)

Answer 21

1) For genes with reduced penetrance, need greater sample size
2) Need to replicate studies for validation
3) Need to demonstrate cause, not just correlation. This requires research on specific mechanisms, which GWAS don’t do

Question 22

CF genetic modifiers which affect lung function
1)
2)
3)

Answer 22

1) EDNRA
2) MBL2
3) TGFb1

Question 23

Which aspect of CF phenotype do EDNRA, MBL2 and TGFb1 affect?

Answer 23

Lung function (FEV1)

Question 24

What does EDNRA encode?

Answer 24

Endothelin receptor type A

Question 25

Correlation between endothelin receptor type A and CF phenotype

Answer 25

Variants in EDNRA alter smooth muscle tone and vasculature in airways

Question 26

What does MBL encode?

Answer 26

Mannose binding lectin

Question 27

How is mannose binding lectin implicated in CF phenotype?

Answer 27

Defective MBL results in reduced innate immunity, and more severe bacterial infections in lungs

Pseudomonas aeruginosa main bacterial threat

Question 28

How is TGFb1 implicated in CF phenotype?

Answer 28

TGFb1 involved in inflammation and tissue remodelling

Higher levels correlate with worse phenotype

Question 29

Which aspect of CF phenotype does MSRA exacerbate?

Answer 29

GIT blockage

Question 30

Which mutation correlates with worse GIT blockage in CF?

Answer 30

MSRA (methionine sulphoxide reductase)

Question 31

How does MSRA correlate with CF phenotype?

Answer 31

MSRA encodes methionine sulphoxide reductase
Methionine sulphoxide reductase modifies intestinal enzymes, EG: alpha-1 antitrypsin

Modification can lead to intestinal blockage, modified digestion

Question 32

Which mutation correlates with diabetes in CF?

Answer 32

TCF7L2

Question 33

Which phenotype correlates with TCF7L2 in CF?

Answer 33

Diabetes

Question 34

How does TCF7L2 correlate with diabetes in CF?

Answer 34

TCF7L2 (transcription factor 7-like 2) plays role in proliferation and function of beta-cells in pancreatic islets

Question 35

Which environmental factors correlate with worse CF outcomes?
1)
2)
3)
4)

Answer 35

1) Being female
2) Lower socio-economic status
3) Exposure to tobacco smoke
4) Disease exposure

Question 36

Why mightn’t being female be merely a genetic predisposition to worse CF phenotype?

Answer 36

CF requires a high-fat, high-salt diet.

Young women more likely to care about weight, therefore maybe less likely to follow diet

Question 37

Cascade testing

Answer 37

Test relatives of newborn with CF

Question 38

Newborn screening for CF
1)
2)
3)

Answer 38

1) Immunoreactive trypsinogen test
2) If in top 1% of IRT levels, DNA testing on 12 mutation panel
3) Heterozygotes have sweat test of NaCl concentration

Question 39

Immunoreactive trypsinogen test

Answer 39

If baby has CF, levels of immunoreactive trypsinogen will probably be high
If baby has [IRT] in top 1%, given DNA testing

Question 40

DNA testing for CF

Answer 40

Initial screen is for 12 mutations

If 2 mutations aren’t detected, extended DNA test is used

Question 41

Positive result for sweat test

Answer 41

Over 60mmol/L of NaCl

Question 42

Equivocal result for sweat test

Answer 42

30-60mmol/L of NaCl

Question 43

Negative result for sweat test

Answer 43

Under 30 mmol/L of NaCl

Question 44

Procedure for sweat test

Answer 44

1) Pilocarpine (ionophore) placed on arm to produce sweat

2) Sweat is collected, sent to a lab

Question 45

When is the sweat test performed?

Answer 45

At 6 weeks of age

If a baby has scored in the top 1% of [IRT], hasn’t been found to be homozygous for a CF mutation

Question 46

Carrier testing offered by doctors in Victoria

Answer 46

$200
12 mutations, tested from a cheek swab
Can test for more mutations

Question 47

VCCS reproductive carrier screen

Answer 47

Includes CF, fragile X syndrome, PKU
Costs $385
From a blood sample

Question 48

Options for carrier parents

Answer 48

Pre-implantation genetic diagnosis

Implant unaffected embryos