Prenatal Anomaly Screening and Diagnosis

1. Overview and Principles

Thompson & Thompson Genetics and Genomics in Medicine, 9th ed.

2. First-Trimester Screening (11–13+6 weeks)

2a. Combined First-Trimester Test

Creasy & Resnik's Maternal-Fetal Medicine, Principles and Practice

2b. Nuchal Translucency (NT) Measurement

Proper caliper placement for NT measurement. (From Nicolaides KH, 1999)

• Detailed first-trimester anatomy scan + echocardiogram at 13–14 weeks
• Repeat second-trimester scan + echo
• Chromosomal microarray (detects pathogenic CNVs in ~4–7% of isolated elevated NT cases)
• RASopathy/Noonan syndrome panel (pathogenic variants found in ~5.2% when NT >4 mm; incidence rises to ~1:90 vs. population 1:1,000)
• Consider whole-exome sequencing if additional anomalies present

2c. First-Trimester Ultrasound Markers

• Nasal bone (NB) absence: Absent in ~25% of Down syndrome fetuses (vs. 0% of euploid controls in some series). Adds independent screening value to NT + biochemistry.
• Ductus venosus flow, tricuspid regurgitation: Additional soft markers used in specialist centers.

3. Second-Trimester Screening (14–20 weeks)

MSAFP at 16 weeks (log scale, MoM) — unaffected vs. open spina bifida. Cutoff ≥2.5 MoM triggers further investigation. (Emery's Elements of Medical Genetics)

4. Non-Invasive Prenatal Testing (NIPT) / Cell-Free Fetal DNA (cffDNA)

1. Massively parallel shotgun sequencing (MPSS) — sequences all genomic fragments, identifies chromosomal origin of each
2. Targeted (chromosome-selective) sequencing — focuses on chromosomes 13, 18, 21, X, Y; reduces cost ~10-fold and enables benchtop sequencers

Creasy & Resnik's Maternal-Fetal Medicine

• NIPT is a screening test, not diagnostic — positive results require confirmatory invasive testing
• Relies on adequate fetal fraction (typically ≥4%); low fetal fraction (obesity, early GA) can cause no-call results
• Cannot reliably detect all structural anomalies or single-gene disorders
• 22q11.2 deletion testing by cffDNA is available but has lower sensitivity/specificity than microarray

5. Invasive Diagnostic Procedures

5a. Indications (Box 18.1 — Thompson & Thompson)

• Patient preference / wishes for diagnostic certainty
• Positive maternal screening result (serum, NT, NIPT)
• Advanced maternal age (now offered to all, not age-restricted)
• Family history of chromosomal abnormality
• Previous child with trisomy or unbalanced chromosomal rearrangement
• Parent known to carry a chromosomal rearrangement (inversion, translocation)
• Elevated NT + normal NIPT (microarray + karyotype indicated)
• Risk for a specific single-gene disorder (CF, thalassemia, Huntington's, etc.)
• Fetal structural anomaly on ultrasound

5b. Chorionic Villus Sampling (CVS)

• Timing: 10–13 weeks
• Route: Transcervical or transabdominal
• Advantage: Earlier result than amniocentesis (first trimester)
• Cells analysed: Cytotrophoblast (rapid, lower resolution) vs. mesenchymal core (long culture, higher resolution, more representative of fetal lineage)
• Result time: Short-term culture result in days; long-term culture 10–14 days
• Complications: Procedure-related fetal loss ~1 in 450 (≈ background 2–5%); limb reduction defects reported historically but not confirmed in large series performed >10 weeks GA by experienced physicians
• Mosaicism: ~1% of CVS yield ambiguous mosaicism — follow-up amniocentesis may be needed

5c. Amniocentesis

• Timing: Typically 15–18 weeks (can be earlier or later)
• Cells analysed: Amniocytes (fetal cells in fluid); cultured for 10–14 days for karyotype
• Lower mosaicism rate than CVS
• Also used for: AFP in amniotic fluid (NTD diagnosis), viral studies, enzyme assays
• Procedure-related fetal loss: ~1 in 450 (comparable to CVS in experienced centres)

6. Laboratory Studies on Fetal Samples

7. Carrier Screening

• Previously: Targeted by ancestry — thalassaemia (Mediterranean/Asian), sickle cell (African), cystic fibrosis (Northern European), Ashkenazi Jewish panel (Tay-Sachs, CF, familial dysautonomia, Canavan, Gaucher, etc.)
• Now (ACOG recommended): Broad pan-ethnic carrier screening panels covering >200 conditions, regardless of stated ancestry — because precise ancestry is increasingly difficult to assign

Thompson & Thompson Genetics and Genomics in Medicine, 9th ed.

8. Second-Trimester Anatomy Scan (18–22 weeks)

9. Prenatal Diagnosis of Specific Conditions

Neural Tube Defects

• MSAFP ≥2.5 MoM at 16 weeks → detailed ultrasound / fetal anatomy scan
• "Lemon sign" (frontal bossing) and "banana sign" (cerebellum) on ultrasound are hallmarks of open spina bifida
• Amniocentesis for amniotic fluid AFP + acetylcholinesterase can confirm open NTD

Haemoglobin Disorders

• Sickle cell disease, thalassaemia: DNA-based diagnosis on CVS or amniocyte DNA
• Carrier couples identified on preconception / first antenatal visit screening → offered invasive testing

Single-Gene Disorders

• CF (CFTR), SMA (SMN1 deletion), Huntington's (CAG repeat), Duchenne MD (dystrophin)
• Preimplantation genetic testing (PGT) is an alternative avoiding the need for pregnancy termination

10. Genetic Counselling

1. Obtain accurate three-generation pedigree
2. Offer pre-test and post-test counselling for all screens and diagnostic tests
3. Clarify the distinction between screening and diagnosis
4. Present options non-directively, respecting autonomy, cultural and religious values
5. Discuss the limitations of each test — no test excludes all abnormalities

• Implications of positive/negative/uncertain results (variants of uncertain significance — VUS)
• Reproductive options: continuation of pregnancy, termination, adoption, fetal therapy
• Family implications (carrier status of parents and siblings)

11. Fetal Therapy — When Diagnosis Leads to Intervention

Thompson & Thompson Genetics and Genomics in Medicine, 9th ed.

Summary: Screening vs. Diagnostic Pathway

All pregnant women
        │
        ├──► CARRIER SCREENING (preconception / early 1st trimester)
        │        Pan-ethnic expanded panel
        │
        ├──► 1ST TRIMESTER COMBINED TEST (11–13+6 weeks)
        │        NT + free β-hCG + PAPP-A + maternal age
        │        Detection ~88% for T21 (5% FPR)
        │
        ├──► NIPT / cffDNA (from ~10 weeks)
        │        T21 DR 99.7%, T18 DR 97.9%
        │        Positive → confirm with invasive testing
        │
        ├──► ANATOMY SCAN (18–22 weeks)
        │        Structural anomaly detection
        │        AFP for NTD (if 2nd trimester serum screen)
        │
        ↓ High-risk screen result, anomaly, family history
        
INVASIVE DIAGNOSTIC TESTING
   CVS (10–13 wks)   or   Amniocentesis (≥15 wks)
         │
         ├─ Karyotype (5–10 Mb resolution)
         ├─ CMA / microarray (50–100 kb, recommended routinely)
         ├─ FISH (rapid, targeted)
         ├─ Single-gene / panel testing
         └─ WES/WGS (structural anomalies + normal karyotype/CMA)

• Creasy & Resnik's Maternal-Fetal Medicine, Chs. 30–31
• Thompson & Thompson Genetics and Genomics in Medicine, 9th ed., Ch. 18
• Emery's Elements of Medical Genetics and Genomics, Ch. 20
• Buijtendijk et al. (2024). Diagnostic accuracy of ultrasound screening for fetal structural abnormalities — Cochrane Database Syst Rev. PMID: 38721874