A homozygous F508del fetus and a 'non-carrier' father
Yael, 29, is pregnant for the first time. Her older brother has cystic fibrosis (CF), and she has been found to carry the F508del variant in CFTR. Her partner, Amir, 31, had a commercial carrier-screening panel covering 30 common CFTR variants, all reported negative; the panel has a detection rate of about 90% in his ethnic group. Both are healthy.
At 12 weeks, chorionic villus sampling is performed and the laboratory reports the fetus as homozygous F508del. The sample was checked for maternal contamination and passed. The laboratory report states that "both parents must be carriers".
Yael asks whether the result means that Amir is the father, and whether the same thing will happen in a second pregnancy. Both families are involved in the discussion, and the laboratory has retained the DNA samples.
1. The report's statement is an inference, not an observation. List at least three explanations consistent with a homozygous F508del fetus and a negative paternal panel, rank them, and give one test that distinguishes each.
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What the result actually says: both of the fetus's CFTR copies carry F508del. What follows from that depends on where the second copy came from.
- Maternal uniparental isodisomy of chromosome 7 - the fetus inherited two copies of Yael's F508del chromosome and no paternal chromosome 7. This produces homozygosity with a genuinely non-carrier father. Test: STR genotyping of fetus and both parents across chromosome 7; look for absent paternal alleles and homoallelism at maternal markers. Because matUPD7 also causes Silver–Russell syndrome, fetal growth should be monitored.
- Genotyping or laboratory error - allele dropout in Amir's test (a polymorphism under a primer site) or a sample swap, despite the contamination check. Test: re-draw and re-test Amir with a different method (allele-specific PCR plus Sanger sequencing of the F508del region), and re-genotype the fetus from an independent amniocentesis sample with identity markers.
- De novo F508del on the paternal chromosome - extremely rare (order of 10⁻⁸ per base per generation) but formally possible. Test: paternity markers plus sequencing of the paternal chromosome to show the mutation is absent in his somatic DNA.
- Non-paternity - raised neutrally by the counsellor and tested with informative markers.
What does not explain it: Amir carrying a different CFTR variant missed by the panel would make the fetus compound heterozygous, not homozygous F508del. The homozygosity itself is the decisive observation and rules that explanation out.
2. What is the recurrence risk for a second pregnancy under each explanation, and what should the couple be told before the confirmatory results are available?
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Risk by explanation:
- Amir truly carries F508del and the panel was falsely negative: 25% per pregnancy, with prenatal or preimplantation testing offered each time.
- Maternal UPD 7: very low (<1%), because UPD is usually a sporadic error; but Yael's chromosome 7 should be karyotyped, since a structural rearrangement would change the figure.
- De novo mutation: negligible, well below 1%.
- Laboratory error: unknown until the correct genotypes exist - possibly 25%.
What to say now: the honest answer is a range, from near zero to one in four, and that the confirmatory tests are what turn the range into a single number. Giving 25% immediately would be wrong if the cause is UPD; giving "no risk" would be wrong if the cause is a missed paternal allele.
The other half of the counselling: if the homozygous result is confirmed, the fetus is a patient. The couple should be referred to a CF centre for pancreatic enzymes, airway clearance and genetic counselling, and told that CF care has changed prognosis substantially. The reproductive decision and the medical plan are separate conversations, and both should follow the confirmation, not precede it.
3. Yael asks whether a negative carrier panel could still be hiding carrier status. Calculate the residual risk using a carrier frequency of 1/25 and 90% detection, and explain what a detection rate does and does not mean.
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Calculation. Prior probability of being a carrier = 1/25 = 0.04; prior odds carrier : non-carrier = 0.04 : 0.96. A negative panel is 10 times less likely in a carrier than in a non-carrier (10% of carriers are missed).
Posterior = (0.04 × 0.1) / [(0.04 × 0.1) + 0.96] = 0.004 / 0.964 ≈ 0.0041, about 1 in 240.
For a couple with one known carrier, risk of an affected child = 0.0041 × 0.25 ≈ 0.1%, roughly 1 in 1,000.
Interpretation. A 90% detection rate is a property of the panel applied to a population; it is not a statement about one individual. Residual risk after a negative panel is reduced, never zero, and it is highest when the partner comes from an ethnic group the panel represents poorly. This is also why a negative panel is not a substitute for testing when the family history already indicates a variant: in this pregnancy the fetus is homozygous, so the prior arithmetic is irrelevant - the result itself is the finding that must be explained by UPD, de novo mutation or laboratory error.