Prenatal Diagnosis

Chorionic villus sampling (CVS) and amniocentesis are ways to collect a sample, not tests in themselves.

What matters is the type of genetic test performed on the sample: PCR, FISH, karyotype, microarrays, exome, whole genome sequencing (WGS), gene-specific sequencing

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Diagnostic Tests for High NT

Opinion: monogenic conditions must be targeted

Diagnostic testing (CVS or amniocentesis) examines fetal genetic material directly and can provide a definitive diagnosis for the conditions tested, rather than a risk estimate. The choice between CVS (from 11 weeks) and amniocentesis (from 15 weeks) depends on timing and the specific test required.

Increased nuchal translucency (NT) is a phenotype linked to a broad differential, many causes being rare, sporadic and de novo. To be truly diagnostic rather than merely invasive, the genetic assay must address the full differential, including monogenic disorders. A test that does not evaluate monogenic disease is not diagnostic.

Twenty years ago, karyotyping was considered diagnostic. By 2026, a truly diagnostic genomic work-up for high NT should include exome or whole-genome sequencing (WGS).

Genomics alone cannot exclude isolated structural anomalies; a targeted, expert ultrasound is still required to identify or rule these in or out.

CVS 

Chorionic Villus Sampling (CVS): From 11 weeks, a tiny placental sample (chorionic villi) is taken for chromosome and gene tests. It is placental DNA, not fetal. Small miscarriage risk.

Amniocentesis

Amniocentesis: From 15 weeks, a small amount of amniotic fluid with fetal cells is taken for chromosome and gene tests. Small miscarriage risk (usually a little lower than CVS).

Prenatal diagnostic testing

What happens during an invasive test?

Most invasive prenatal tests are performed through the maternal abdomen (transabdominal) under continuous ultrasound guidance in a clinic setting.
After cleaning the skin, the clinician inserts a thin needle into maternal abdomen (tummy) to obtain a sample: CVS takes a tiny piece of placental tissue; amniocentesis draws a small amount of amniotic fluid. The needle is guided away from the baby and the placenta is approached only as needed; the whole procedure typically takes a few minutes.
Fetal heartbeat is checked before and after, and patients are advised to rest for the remainder of the day. Mild cramping or spotting can occur, and there is a some procedure-related risk of miscarriage, or infection.

Tests for increased NT

Done on CVS or amniotic fluid samples

Standard diagnostic tests - chromosomal anomalies:
- QF-PCR - a rapid check for Down, Edwards and Patau syndromes)
- chromosomal microarray - looks for missing or extra pieces of chromosomes)
Gene level tests - monogenic syndromes:
- exome (WES) - gene coding variants
- whole-genome sequencing (WGS) - the broadest genetic test

Genetic results should be integrated with a targeted expert ultrasound, and confirmatory or follow-up tests may be needed in specific scenarios.

QF-PCR

Rapid test for common trisomies (21,18,13)

QF-PCR is a rapid assay performed on CVS or amniotic fluid for fetuses with increased NT. It provides a fast result (24-72 hours) for common aneuploidies: Down syndrome (T21), trisomies 18 and 13, and sex chromosome abnormalities, and can also suggest triploidy. Results can be affected by maternal cell contamination. In practice, QF-PCR is used as a rapid first-line test and is paired with microarray and, when indicated, exome or whole-genome sequencing for a truly diagnostic work-up.

Chromosomal microarray

Microdeletions and microduplications

Chromosomal microarray (CMA or aCGH/SNP array) is a standard genetic test that detects microdeletions and microduplications (missing or extra pieces of chromosomes). Microarray results usually return in about 1-2 weeks.
CMA does not detect most single-gene sequence variants (monogenic syndromes) and has other limitations.
In practice, it’s a first-line diagnostic test for increased NT when aneuploidy is excluded by QF-PCR or when a scan suggests a structural anomaly.

Exome sequencing (WES)

Monogenic syndromes ~ 20,000 genes

Whole-exome sequencing (WES) targets the protein-coding regions (exons) of ~19,000–20,000 human genes, which make up only ~1–2% of the genome yet harbour the great majority of known Mendelian disease-causing variants (often quoted ~85%).
Some services instead run a “clinical exome”, focusing on roughly 4,000–7,000 disease-associated genes, it is cheaper and quicker.
Because many causes of increased NT are monogenic and spread across thousands of genes, exome examines the coding genome to find diagnoses that QF-PCR/CMA miss and to guide prognosis and management.

Whole-genome sequencing

The most thorough test of fetal DNA

Whole-genome sequencing (WGS) reads almost all of the fetal genome (≈3.1–3.2 billion bases), covering both coding and non-coding DNA regions, and often includes the mitochondrial genome.
It detects single-gene variants, small indels, and many copy-number and structural variants, offering broader coverage and more uniformity than exome. WGS still has limits, so a normal result does not exclude all disease.
WGS is the most expensive genetic test for increased NT. It offers a broader yield than exome testing, especially valuable in this situation, where the differential diagnosis of genetic syndromes is wide.

Single-gene testing

PCR/Sanger/NGS panels

After a high-chance monogenic result on extended NIPT for increased NT, confirmation is done with targeted single-gene testing on CVS or amniotic fluid: PCR/Sanger sequencing to verify the specific SNV/indel flagged, or a focused NGS gene panel when several genes could explain the phenotype. This is diagnostic (not a screen), often run as a trio to assess inheritance, and provides definitive confirmation to guide prognosis and counselling.

Frequently
Asked Questions

What's the diagnostic toolbox for prenatal genetics today; how do the tests compare?

QF-PCR (rapid aneuploidy screen): CVS/amnio; fast (same day–48 h) detection of T13, T18, T21 and sex-chromosome aneuploidy; can suggest triploidy.
Karyotype (G-banded): Whole-chromosome changes and large/balanced rearrangements; limited resolution; slow.
Chromosomal microarray (CMA; aCGH/SNP array): Genome-wide CNVs (~50–100 kb+); SNP arrays also assess ROH/UPD; cannot detect most single-gene variants or balanced rearrangements.
Targeted FISH: Rapid confirmation of suspected aneuploidies/rearrangements or specific microdeletions; locus-specific.
MLPA / MS-MLPA: Targeted exon-level CNVs; methylation/imprinting disorders (e.g., PWS/AS, BWS/SRS).
Single-gene testing (PCR/Sanger/NGS panels): For known familial variants or phenotype-driven monogenic disorders.
Exome sequencing (WES, ideally trio): Coding regions; SNVs/indels and some CNVs; phenotype-guided interpretation.
Whole-genome sequencing (WGS, ideally trio): Coding + non-coding; SNVs/indels/CNVs/selected SVs; best single comprehensive assay; may still miss repeats/methylation.
Low-pass (shallow) WGS: Genome-wide CNV/aneuploidy assessment; not suitable for monogenic variant detection.
Mitochondrial genome sequencing: mtDNA variants with heteroplasmy quantification; trio/segregation useful.
UPD studies (SNP array/STRs): Confirms uniparental disomy where suspected (imprinting/ROH patterns).
Quality checks: Maternal cell contamination and confined placental mosaicism assessment (STRs/array metrics); essential for result validity.

Why do I need to send my scan before doing the NIPT?

We ask you to send us your scan so our medical team can confirm that you’re at least 10 weeks pregnant and that the pregnancy appears to be developing normally. This helps us ensure the test is appropriate and that the results will be accurate. It’s also important to understand that NIPT only screens for specific genetic conditions. It does not detect structural anomalies, such as heart defects or issues with organ development, which are physical rather than genetic. These types of conditions are usually picked up later in pregnancy through detailed ultrasound scans. Sending your early scan allows our doctors to check for any concerns before moving forward with the NIPT.

Can NIPT tell me the sex of my baby?

Yes, NIPT can usually identify the baby’s biological sex with high accuracy, but this is completely optional. If you’d like to know, just let your genetic counsellor know during your consultation — and if you’d rather not find out, we’ll make sure it’s not included in your report.

Is NIPT covered by the NHS?

At the moment, NIPT is only offered through the NHS in certain cases — for example, if you’ve had a high-risk result from a standard screening test. At Jeen, we offer private NIPT testing with flexible options, fast results, and full clinical support, including at-home appointments and expert guidance.

How long does it take to get results?

Your results will usually be ready within 2–10 working days from the time your sample arrives at our partner lab. The exact turnaround time depends on which NIPT you’ve chosen and the location of the laboratory. We’ll keep you informed throughout the process and arrange a follow-up consultation to talk you through your results as soon as they’re ready.

Please note that delays can occur during public holidays in both the UK and the US. If your results indicate that follow-up testing is needed for your partner, we’ll act quickly to keep everything moving smoothly. Our priority is to get you the answers you need without unnecessary delays — so you can make confident, informed decisions for your pregnancy.

When can I take the NIPT and is it safe?

You can take the NIPT from 10 weeks into your pregnancy. Before booking your test with Jeen, we ask you to send us a recent pregnancy scan, such as a dating or viability scan, so our team of specialists can confirm you’re eligible to proceed.

Yes, NIPT is completely safe for both you and your baby. It’s a non-invasive blood test that only requires a small sample from your arm, and there is no physical contact with the baby. This means there is no risk of miscarriage or harm to the pregnancy, unlike some invasive procedures.

How accurate is NIPT?

NIPT is over 99% accurate at detecting Down’s syndrome and also highly reliable for Edwards’ and Patau’s syndromes. It is more accurate than standard NHS screening and produces fewer false positive results, which means fewer people are sent for unnecessary follow-up testing.

Do I need genetic counselling before NIPT?

Yes, at Jeen we believe it’s important that everyone taking NIPT has a chance to speak to a qualified genetic counsellor first. This session helps you understand what the test covers, what it doesn’t, and what the results might mean for you and your baby. It’s a space to ask any questions and make confident, informed choices.

What happens if my NIPT result is high risk?

If your result shows a high risk for a condition, we’ll arrange a follow-up session with one of our genetic counsellors to explain exactly what it means. You’ll be given the option to have a diagnostic test, such as amniocentesis or CVS, which can confirm the result. We’ll support you at every step, with clear information and no pressure.

Will NIPT detect all possible conditions?

No, NIPT screens for a specific set of genetic conditions, mostly involving extra or missing chromosomes. It won’t detect all birth defects or structural anomalies, such as heart defects or limb differences. That’s why it’s important to still attend all your routine scans and check-ups during pregnancy.

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