Consult your textbook and trustworthy Internet sites to answer the following questions: 1. Which organs are affected by cystic fibrosis? What are the disease symptoms? Organs that are affected by cystic fibrosis include the lungs, pancreas, liver, sweat glands, reproductive organs, nose and sinuses. The symptoms of cystic fibrosis include coughing with mucus coming up, wheezing, breathlessness, decrease in ability to exercise, lung infections, inflamed nasal passages, stuffy nose, bad growth, intestinal blockage, severe constipation and greasy foul smelling stool.
2. Draw a pedigree showing the family history for CF in Sarah’s and Michael’s families. Be sure to distinguish between individuals with the disease, those that are carriers for the disease, and individuals who do not possess a copy of the disease allele. Sarah’s FamilyMichael’s Family
Part II Questions: Punnett Squares
3. Construct a Punnett square to demonstrate why Sarah concluded that she and Michael could not have an affected child (assuming that she does not carry a CF mutation). Since Sarah jumped to the conclusion that she did not carry any recessive alleles for CF she thought that her and Michael’s baby wouldn’t have CF. So when you cross what she thought she had CC with Michael’s carrier genotype Cc you will have a baby with a 50% chance of being normal and 50% of being a carrier, but would not have CF. The cross between Cc x CC is shown below.
4. If Sarah were a carrier, what would be the chance that she and Michael would have an affected child? Show the Punnett square. There is a 50% chance that the baby will be a carrier. 25% chance that the baby is going to be normal. Then there is a 25% chance that the baby will have CF.
Part III Questions: CFTR Mutations
5. Look closely at the section on “Allelic Variants.” Is the delta-F508 mutation the only known alteration of the CFTR gene? No delta-F508 mutation is only one of many alteration of the CFTR gene. For example other alterations are 6. As you look at the list of Allelic Variants (starting with .001), how does the information in brackets (e.g., [CFTR, PHE508DEL]) describe each mutation? This information describes what amino acid is located where the mutation was located.
In this case the amino acid is phenylalanine. It tells us the codon where the mutation took place. In this example the mutation is at codon 508. This information also tells up what type of mutation took place. In this case it was a deletion mutation. 7. The CFTR gene contains how many exons? How many introns? Sketch a rough diagram of the exon/intron structure of the CFTR gene. There are 27 exons in the CFTR gene. There are 26 introns in the CFTR gene. Here’s a sketch of a rough diagram of the exon/intron structure of the CFTR gene. Blue rectangles are introns white are exons.
8. For each mutation (allelic variant) listed below, explain how the mutation would affect the production of (1) the mRNA and (2) the protein encoded by the CFTR gene. As an example, the first case is completed for you.
• .0001 CYSTIC FIBROSIS [CFTR, PHE508DEL]
The 508th triplet codon, which normally codes for phenylalanine, is deleted. Consequently, the CFTR mRNA is 3 nucleotides shorter than normal, and the CFTR protein is one amino acid shorter, missing its 508th unit.
• .0003 CYSTIC FIBROSIS [CFTR, GLN493TER]
There was a G to T change in nucleotide 1609 in exon ten. The effect of this nucleotide change mutation was a premature stop codon created at position 493.
• .0004 CYSTIC FIBROSIS [CFTR, ASP110HIS]
A C to G change in the nucleotide sequence in the fourth exon caused the mutation. The result of this mutation was a change from an aspartic acid residue to a histidine one.
• .0019 CYSTIC FIBROSIS [CFTR, 2-BP INS, 2566AT]
This mutation was from an insertion of two nucleotides. AT was inserted right after nucleotide 2566 on exon 13. This resulted overall in a frame shift mutation.
• .0008 CYSTIC FIBROSIS [CFTR, IVS10, G-A, -1]
This was a splice mutation that changed nucleotide-1 in intron number ten from G to A. As a result a splice site was destroyed.
• .0064 CYSTIC FIBROSIS [CFTR, IVS12, G-A, +1]
A G to A switch in nucleotides at the position 1 donor site caused skipping over exon 12
. • .0123 CYSTIC FIBROSIS [CFTR, 21-KB DEL]
This is a large mutation. This mutation deletes 21,080 bp ranging from exon 1 to exon 3. This resulted in deletion of exon 2 and exon 3. This large deletion also caused a premature termination signal in exon 4. 9. Sarah wondered how all these different mutations can cause the same disease. As the genetic counselor, how would you explain this to Sarah and Michael? All these different mutation can cause the same disease because they all occur on the CFTR gene. Even if one amino acid is changed on the CFTR there is going to be a possibility of cystic fibrosis occurring. Also different mutations can cause different severities and traits of cystic fibrosis.
Part IV: The Test
Read the following research article to learn about the test used for CF genotyping, then answer the questions below. Strom et al. 2006. “Technical Validation of a Tm Biosciences Luminex-Based Multiplex Assay for Detecting the American College of Medical Genetics Recommended Cystic Fibrosis Mutation Panel.” Journal of Molecular Diagnostics 8: 371-375. 10. How many different mutations had been found in the CFTR gene when this article was written? There have been over 1400 mutations found in the CFTR gene when this article was written. 11. How many of these CFTR mutations can be detected by the Tag-It CFTR 40 + 4 Luminex-based reagent system from Tm Biosciences? 40 mutations and 4 polymorphisms can be detected by the Tag-It 40+4 Luminex-based reagent system. There were two mutations that were removed from the 25 mutation original panel though; I148T and also 1078delT.
There are 40 mutations that can be detected by this test, but two were removed because one of the mutations was decided to be a polymorphism and the other was too rare to test for. 12. What criteria did researchers use when determining which mutations to include in the Tag-It test? Researchers used a Luminex bead system which develops reagents for multiplex molecular analyze. By using this bead system, the researchers were able to tell that this analysis showed that it detected the 25 mutations on the original reagent. These 25 mutations were then looked at by researchers. Two of the mutations were decided to be thrown off the original list.
The reason was one of the mutations turned out to be a polymorphism and the other mutation was so rare that the researchers decided to throw it out. Then 15 of the mutations are considered to be supplementary mutations. This means that they can be tested for by the Tag-It 40 + 4 test but, aren’t on the ACMG screening panel. So there are a total of 23 mutations on the revised Tag-It 40+4 carrier test. 13. What is the chance that Sarah is actually a carrier for a CFTR mutation, even though her Tag-It test results came back negative? There is a chance that Sarah is actually a carrier for a CFTR mutation, but very unlikely. The chances are small that Sarah is actually a carrier for a CFTR mutation.
14. As the genetic counselor, explain to Sarah and Michael why you said “not exactly” when Sarah asked if it was safe to conceive a child. There are more mutations on the gene than you were screened for. We didn’t test the ones that are so rare, because the possibility of you having them is very low. There is a chance that you could be a carrier, but it is very unlikely. So there is a chance that your child could have CF because Michael is a carrier and we aren’t for sure you’re not a carrier, but it isn’t very likely that your child will have CF. 22. (Zack)
If I was in this situation, I would chose to adopt a child. The reason is there is a risk of having a baby with CF, and I wouldn’t want to take that small chance. 22. (Krickett) It seems to me that Sarah and Michael really want to have a child of their own. So, if I was them I would choose to get pregnant and continue with the pregnancy no matter what. Since there is not really a huge chance of their child getting CF then I would go ahead and see what the outcome would be when having the child.