Lecture 9 - Clinical Genetics of Cystic Fibrosis Flashcards
Incidence of CF
~1/2500 - 3000 live births
Carrier frequency of CF
~1/25 in northern Europe
How strong is the genotype-phenotype correlation in CF?
Strong in some areas (pancreatic insufficiency)
Less strong in other areas (lung blockage)
Which mutation classes correlate with pancreatic insufficiency?
Class I, II and III
Which mutation classes correlate with more severe lung disease?
Classes I, II and III
Which mutation classes correlate with less severe lung disease and pancreatic sufficiency?
Classes IV and V
Example of a mutation in CFTR with reduced penetrance
R117H
What determines R117H penetrance?
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
Why might being heterozygous for CF be advantageous for cholera infection?
If 50% of CFTR channels have impaired function, less water might be lost into the gut lumen
Why might being heterozygous for CF be advantageous for S. typhi infection?
S. typhi can bind to CFTR.
If 50% of CFTR proteins are misshapen, might reduce bacterial adherence
How can environmental vs genetic modifiers be studied for CF?
Compare disease for monozygotic, dizygotic twins, and siblings
How genetically-determined is lung function in CF?
50% genetic, 50% environmental
How genetically-determined is meconium ileus in CF?
Completely genetically determined
How genetically-determined is diabetes in CF?
Mostly genetic
Why identify genetic modifiers of CF? 1) 2) 3) 4)
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
Do many de novo mutations cause CF?
No
Few de novo mutations leading to CF
Ways to identify genetic modifiers of CF
1)
2)
3)
1) Linkage studies
2) Candidate gene association
3) Genome-wide association studies
Linkage studies
Track genes or markers associated with a specific phenotype in individuals or families with CF
Candidate gene association
Look at genes with a known function (which correlates with CF symptoms)
Correlate variations in gene with different CF phenotypes
Genome-wide association studies
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
Drawbacks of genome-wide association studies
1)
2)
3)
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
CF genetic modifiers which affect lung function
1)
2)
3)
1) EDNRA
2) MBL2
3) TGFb1
Which aspect of CF phenotype do EDNRA, MBL2 and TGFb1 affect?
Lung function (FEV1)
What does EDNRA encode?
Endothelin receptor type A
Correlation between endothelin receptor type A and CF phenotype
Variants in EDNRA alter smooth muscle tone and vasculature in airways
What does MBL encode?
Mannose binding lectin
How is mannose binding lectin implicated in CF phenotype?
Defective MBL results in reduced innate immunity, and more severe bacterial infections in lungs
Pseudomonas aeruginosa main bacterial threat
How is TGFb1 implicated in CF phenotype?
TGFb1 involved in inflammation and tissue remodelling
Higher levels correlate with worse phenotype
Which aspect of CF phenotype does MSRA exacerbate?
GIT blockage
Which mutation correlates with worse GIT blockage in CF?
MSRA (methionine sulphoxide reductase)
How does MSRA correlate with CF phenotype?
MSRA encodes methionine sulphoxide reductase
Methionine sulphoxide reductase modifies intestinal enzymes, EG: alpha-1 antitrypsin
Modification can lead to intestinal blockage, modified digestion
Which mutation correlates with diabetes in CF?
TCF7L2
Which phenotype correlates with TCF7L2 in CF?
Diabetes
How does TCF7L2 correlate with diabetes in CF?
TCF7L2 (transcription factor 7-like 2) plays role in proliferation and function of beta-cells in pancreatic islets
Which environmental factors correlate with worse CF outcomes? 1) 2) 3) 4)
1) Being female
2) Lower socio-economic status
3) Exposure to tobacco smoke
4) Disease exposure
Why mightn’t being female be merely a genetic predisposition to worse CF phenotype?
CF requires a high-fat, high-salt diet.
Young women more likely to care about weight, therefore maybe less likely to follow diet
Cascade testing
Test relatives of newborn with CF
Newborn screening for CF
1)
2)
3)
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
Immunoreactive trypsinogen test
If baby has CF, levels of immunoreactive trypsinogen will probably be high
If baby has [IRT] in top 1%, given DNA testing
DNA testing for CF
Initial screen is for 12 mutations
If 2 mutations aren’t detected, extended DNA test is used
Positive result for sweat test
Over 60mmol/L of NaCl
Equivocal result for sweat test
30-60mmol/L of NaCl
Negative result for sweat test
Under 30 mmol/L of NaCl
Procedure for sweat test
1) Pilocarpine (ionophore) placed on arm to produce sweat
2) Sweat is collected, sent to a lab
When is the sweat test performed?
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
Carrier testing offered by doctors in Victoria
$200
12 mutations, tested from a cheek swab
Can test for more mutations
VCCS reproductive carrier screen
Includes CF, fragile X syndrome, PKU
Costs $385
From a blood sample
Options for carrier parents
Pre-implantation genetic diagnosis
Implant unaffected embryos
