Prenatal Genetics
Learning objectives
- LO 1Tell a prenatal screening test from a diagnostic test, and read a screen's accuracy as detection rate, false-positive rate and predictive values.
- LO 2Compare DNA-based and non-DNA-based screens for single-gene disorders and for aneuploidy.
- LO 3Know when prenatal diagnosis is offered, how each sampling method works, and which lab study to run on the sample.
MAPBig-picture map of prenatal testing
LO 1Screening vs diagnostic tests
Q1. Why do prenatal genetic testing at all?
- Reassurance for families at risk
- Preparation for the birth of an affected baby, and for the timing and mode of delivery
- Risk information for couples for whom termination is an option
- In the near future: treatment in utero (stem-cell or gene therapy)
Q2. How is a screening test different from a diagnostic test?
Screening
- Examines low-risk individuals to find those at high risk
- Typically inexpensive and non-invasive (blood, ultrasound)
- Result = a risk, not an answer
Diagnosis
- Determines whether disease is present in a high-risk population
- Usually invasive (amniocentesis, CVS)
- Result = yes or no
ACOG recommends offering both screening and diagnostic tests to all pregnant women, out of respect for patient autonomy.
In-house exam
Screening = low-risk population, non-invasive, cost-effective. Diagnosis = confirms disease in people already identified as high risk (by screening, family history or other factors).
Analogy — the smoke detector and the firefighter
A screen is a smoke detector: cheap, in every house, and sometimes it goes off for burnt toast. A diagnostic test is the firefighter who comes in and checks for an actual fire.
Q3. Which patients choose screening?
The patient's attitude is the most important determinant of whether she takes up screening.
| Type | Attitude | What she wants |
|---|---|---|
| Anxious | High anxiety | Testing irrespective of risk (goes straight to diagnosis) |
| Balance | Weighs risks | A risk estimate before considering invasive testing → best candidate for screening |
| Content | Declines | Refuses both screening and diagnosis |
Memory tool
A-B-C: Anxious wants it all, Balance wants the screen, Content wants nothing.
Q4. How do I describe a screen's accuracy?
| Affected | Normal | ||
|---|---|---|---|
| Test abnormal | a | c | a + c |
| Test normal | b | d | b + d |
| a + b | c + d |
| Measure | Formula | Meaning |
|---|---|---|
| Detection rate (= sensitivity) | a / (a + b) | Affected fetuses the screen catches |
| False-positive rate | c / (c + d) | Normal fetuses falsely flagged |
| Positive predictive value | a / (a + c) | Chance a positive screen is truly affected |
| Negative predictive value | d / (b + d) | Chance a negative screen is truly normal |
Detection and false-positive rates must be translated into predictive values: that's what the patient actually needs to know.
Trap
Detection rate and FPR describe the test; PPV depends on the prevalence too. A near-perfect test can still have a modest PPV when the disease is rare.
Q5. Why can a 99% detection rate give a PPV of only 66%?
- With detection ≈100%, one false positive among 998 normals still makes up a third of all positives
High yield
When a patient gets a result, what matters is the chance it's correct: PPV for a positive, NPV for a negative. A positive screen always needs diagnostic confirmation.
ApplyLO 1 application questions
A1A screen catches 95 of 100 affected fetuses and flags 50 of 10,000 normal ones. Detection rate, FPR and PPV?
A2A patient weighs her risk carefully and wants numbers before deciding on amniocentesis. Which type is she?
LO 2DNA vs non-DNA screening
Q1. How do non-DNA screens find single-gene disorders?
- Family history of an affected individual
- Family history of female infertility, premature ovarian failure, unexplained intellectual disability, developmental delay or autism → risk factors for Fragile X
- Ethnicity (ACOG): all ethnicities → SMA and CF; Ashkenazi Jewish → a panel that includes Tay-Sachs
Step 1
Fragile X premutation carriers (55–200 CGG repeats) get premature ovarian insufficiency (women) and FXTAS (older men); full mutation (>200) → intellectual disability, autism, macroorchidism.
Q2. What does an NGS expanded carrier screen add?
- Done pre-conception or early in pregnancy on saliva or blood from both parents
- Screens for >100 single-gene disorders; applicable to all ethnic groups
- Both parents carriers for the same AR condition → 25% risk of an affected fetus → offer invasive diagnosis
- Detects 3× as many carriers as ethnicity-based screening; outperforms it across every racial/ethnic group
- 24% of individuals carry at least one non-mild condition, but <1% of couples carry the same one
- Ethnicity misleads: ≈½ of Tay-Sachs carriers had no Jewish ancestry; many "ethnic" disorders are widely distributed
| Ideal panel condition (ACOG / ACMG) |
|---|
| Carrier frequency ≥1:100 |
| Well-defined phenotype; severe |
| Early-childhood onset |
| Detection rate ≥70% |
| Detrimental effect on quality of life: cognitive or physical impairment, need for surgical or medical intervention |
Only 27% of conditions on commercial panels meet these criteria.
High yield
Expanded carrier screening beats ethnicity-based screening. A Tay-Sachs carrier may have no Jewish ancestry.
Trap
A carrier screen tests the parents, not the fetus. Two carrier parents still need diagnostic testing of the fetus (or PGT) to know whether this pregnancy is affected.
Q3. Which chromosome anomalies are found most often?
- 71% of prenatally diagnosed anomalies are trisomy 21 (≈53%), 18 (≈13%) and 13 (≈5%)
Chromosome anomalies diagnosed prenatally
- T21 + T18 + T13 = 71%
Q4. What are the non-DNA screens for aneuploidy?
| Screen | Key points |
|---|---|
| Family history | Prior child with a chromosome anomaly; parent carrying a balanced translocation |
| Maternal age | Trisomy risk rises sharply after 35, but ≈55% of Down syndrome births are to women under 35 (because most births are) → don't screen by age alone |
| Maternal serum markers (1st or 2nd trimester) | Proteins made by the fetus and/or placenta; aneuploid pregnancies have different levels |
| Sonographic markers | Nuchal translucency (fluid behind the fetal neck) in the 1st trimester |
Maternal age
- Risk climbs after 35, yet 55% of DS births are under 35
Nuchal translucency
- ↑ thickness → ↑ aneuploidy risk
Why it's only a screen
- Curves overlap: NT alone DR ≈55% at 5% FPR
Step 1 — serum marker patterns
| Condition | 1st trimester | Quad screen (2nd trimester) |
|---|---|---|
| Trisomy 21 | ↓ PAPP-A, ↑ β-hCG, ↑ NT | ↓ AFP, ↑ hCG, ↓ estriol, ↑ inhibin A |
| Trisomy 18 | ↓ PAPP-A, ↓ β-hCG, ↑ NT | ↓ AFP, ↓ hCG, ↓ estriol, nl/↓ inhibin A |
| Trisomy 13 | ↓ PAPP-A, ↓ β-hCG, ↑ NT | — |
| Neural tube defect | — | ↑ AFP (+ ↑ amniotic AChE) |
"HIgh" in Down syndrome: hCG and Inhibin go up; everything else goes down.
Q5. How does cell-free DNA screening work?
- Maternal cfDNA comes from normal cell turnover; fetal cfDNA comes from placental apoptosis
- Fetal DNA ≈ 10% of total cfDNA; cleared from maternal blood within hours of birth
- Sequencing assigns each fragment to its chromosome; an excess of chr21 fragments → trisomy 21
Cell-free DNA
- Placental fragments mix with maternal DNA
Counting fragments
- A small excess of chr21 = T21
| Condition | Detection rate | False-positive rate | PPV (age 30) |
|---|---|---|---|
| Trisomy 21 | >99% | 0.2% | 58% |
| Trisomy 18 | 97% | 0.4% | 19% |
| Trisomy 13 | 88% | <1% | 13% |
| Monosomy X | 95% | 1% | — |
Screens for Down syndrome over time
- Non-DNA screens at 5% FPR; cfDNA ≈99% at ≤0.1% FPR
High yield — false-positive cfDNA
- Placental (confined) mosaicism: the DNA is placental, not fetal
- Vanishing twin with an abnormal karyotype
- Maternal mosaicism (e.g., age-related X loss in women >40 → false Turner)
- Maternal transplant or tumor
Trap
cfDNA is a screen, not a diagnosis. Even with >99% detection, a positive T13 result in a 30-year-old is correct only 13% of the time → confirm with amniocentesis.
Memory tool
PPVs fall as the trisomy gets rarer: 21 → 58%, 18 → 19%, 13 → 13% ("13 for 13").
ApplyLO 2 application questions
A1A cfDNA screen shows monosomy X, but amniocentesis shows 46,XX. The mother is 42. Likely explanation?
A2A woman with no Jewish ancestry asks whether she needs Tay-Sachs screening. What does the expanded-panel data say?
LO 3Prenatal diagnosis: indications, methods, lab studies
Q1. When is prenatal diagnosis indicated?
| # | Indication | Note |
|---|---|---|
| 1 | A parent with a structural chromosome abnormality (e.g., balanced translocation) | Fetal risk depends on the type of anomaly and the parent of origin |
| 2 | Previous child with a de novo aneuploidy | Recurrence risk for any chromosome abnormality ≈1/100 |
| 3 | Genetic disorder amenable to prenatal diagnosis | Risk from family history, positive screen (single gene or aneuploidy) or ultrasound findings |
| 4 | Maternal desire to rule out genetic conditions | Offered even when risk is low |
Step 1
≈95% of Down syndrome is meiotic nondisjunction (sporadic; risk rises with maternal age), ≈4% Robertsonian translocation (higher recurrence if a parent carries it), ≈1–2% mosaic.
Q2. How do amniocentesis, CVS and PGT compare?
| Amniocentesis | CVS | PGT | |
|---|---|---|---|
| Sample | Amniotic fluid → fetal cells (skin, urinary tract) | Biopsy of chorion frondosum | Blastomere or 5–8 trophectoderm cells from a blastocyst |
| Timing / route | 2nd trimester; needle under ultrasound | 10–14 weeks; transcervical or transabdominal | Before implantation; requires IVF |
| Fetal loss above background | 1/300–1/500 (background 1–2%) | 0.2–0.3% (background 2–5%) | Biopsy: no ↑ anomalies or adverse outcome to 5 years |
| Advantage | Gold standard; confirms ambiguous CVS/PGT | Early results | Select unaffected embryos |
| Drawback | Rare: feto-maternal hemorrhage, fluid leak, infection | Ambiguous in ≈1% from placental mosaicism → needs amnio | IVF cost and risks; embryo mosaicism; false results 2–5% |
Amniocentesis
- Needle into the amniotic sac; aspirate fluid
CVS
- Transabdominal (left) or transcervical (right)
PGT biopsy
- Day 3 blastomere or day 5–6 trophectoderm
Memory tool
CVS = Chorion, Confusing (mosaic), Come early. Amnio = Answer (the confirmatory test).
Step 1
Amniocentesis is typically done at 15–20 weeks; CVS before 10 weeks has been linked to limb-reduction defects. Amniotic fluid also allows AFP/AChE for neural tube defects.
Trap
An abnormal cell line seen on CVS may be limited to the placenta (confined placental mosaicism). Confirm with amniocentesis before acting on it.
Q3. What are the indications, issues and errors of PGT?
Indications
- Single-gene disorder when both parents are carriers (also HLA matching)
- Structural rearrangement in a couple with a balanced translocation
- Screening for de novo aneuploidy
Issues
- Requires IVF: expensive, intrusive, ovarian hyperstimulation, multiples, adverse outcomes
- Extended culture: 50% of embryos survive to day 3, 25% to day 8; lower implantation after day 6; monozygotic twins with late transfer
| Error | Cause | Consequence |
|---|---|---|
| False negative | Contaminating DNA, allele drop-out (failure to amplify), partial amplification | Abnormal embryo transferred |
| Misdiagnosis | Unprotected sex during IVF, human error (wrong embryo), post-zygotic mitotic changes | — |
| False positive | Embryo mosaicism (16%) | Normal or "self-correcting" mosaic embryos discarded; up to 30% embryo wastage |
- Quoted FP/FN risk 2–5%; the value of PGT for aneuploidy "has yet to be determined"
- Confirm PGT diagnostic results with CVS or (preferred) amniocentesis; continue routine prenatal screening
Trap
Mosaic embryos with 20–50% abnormal cells can still produce healthy children. A "positive" PGT doesn't always mean an affected baby.
Q4. Which lab study do I run on the sample?
| Study | Use | Key numbers |
|---|---|---|
| Karyotype | Traditional standard for aneuploidy and gross rearrangements; used when the indication is a specific aneuploidy or an unbalanced translocation | 10–14 days; FISH quick result in 48–72 h |
| Chromosomal microarray | Fetus with structural anomalies on ultrasound; fetal death needing genetic work-up. Without anomalies, karyotype or microarray may be offered | 5–10% extra yield when karyotype is normal |
| Prenatal exome sequencing | Multiple anomalies with normal karyotype and microarray; a single major anomaly or pattern suggesting a genetic disorder; prior undiagnosed affected fetus/child/stillborn | 20–30% diagnostic yield |
In-house exam
Prenatal exome sequencing: ultrasound shows multiple anomalies and karyotype + microarray are normal. It finds single-gene disorders the other tests miss.
High yield
Microarray and exome need pre- and post-test counseling: variants of uncertain significance (CNVs), non-paternity or consanguinity (SNP arrays), incidental/secondary findings, and re-analysis over time.
Q5. What's coming next?
- cfDNA (NIPT) screening beyond T21/18/13: monosomy X, trisomy 9, unbalanced translocations, large deletions (low PPVs)
- cfDNA diagnosis of single-gene disorders, already reported:
| Inheritance | Disorders |
|---|---|
| AD | Myotonic dystrophy, early-onset primary dystonia, Huntington disease, achondroplasia, Apert, thanatophoric dysplasia, Crouzon |
| AR | Cystic fibrosis, propionic acidemia, Leber congenital amaurosis, sickle cell, β-thalassemia |
| X-linked | Hemophilia A and B |
ApplyLO 3 application questions
A1CVS at 11 weeks shows 47,XX,+16 in some cells. Next step?
A2Ultrasound shows heart, kidney and limb anomalies; karyotype and microarray are normal. Next test?
A3A couple's first child had de novo trisomy 21. Recurrence risk for any chromosome abnormality?
IDImage ID
Image 1 — ultrasound
Image 2 — procedure
Image 3 — procedure
Image 4 — embryo
Image 5 — bar chart
Image 6 — flow
MCQExam-style questions
1Which statement best describes a prenatal screening test?
2A screen for T21 (prevalence 1 in 500) has 99% detection and 0.1% false positives. In 1,000 women, what is its positive predictive value?
3Which patient attitude makes someone the best candidate for a screening test?
4A woman's family includes several women with premature ovarian failure and a nephew with autism. Which disorder should be screened for?
5Compared with ethnicity-based screening, NGS expanded carrier screening:
6Both parents are carriers for the same autosomal recessive disorder on expanded screening. What is the risk to each pregnancy, and what is offered?
7Fetal cell-free DNA in maternal blood comes mainly from:
8A cfDNA screen is positive for trisomy 18, but amniocentesis shows a normal karyotype. Which is the most likely reason?
9What is the main advantage of CVS over amniocentesis?
10The in-house risk of fetal loss attributable to amniocentesis is closest to:
11A fetus has multiple structural anomalies. Karyotype and chromosomal microarray are normal. Best next test?
12A couple uses PGT and discards an embryo reported as aneuploid. Which phenomenon most often makes such a result a false positive?
!Numbers that differ between in-house and Step 1
| Item | In-house | Step 1 / board review |
|---|---|---|
| CVS ambiguous result | Slides: placental mosaicism (class notes say "maternal mosaicism") | Confined placental mosaicism |
| CVS timing | 10–14 weeks | ≈10–13 weeks; before 10 weeks → limb-reduction risk |
| Amniocentesis timing | Not given (2nd trimester) | 15–20 weeks |
| Amniocentesis loss | 1/300–1/500 above 1–2% background | Current estimates ≈0.1–0.3% |
| PGT misdiagnosis | Slides: post-zygotic mitotic changes (class notes say "mitochondrial") | Post-zygotic mitotic errors → mosaicism |
| Microarray indication | Slides: yield 5–10% when karyotype is normal (class notes: "karyotype not yet performed") | First-line for structural anomalies, often instead of karyotype |