How does NIPT work and what can it detect in pregnancy?

Non-invasive prenatal testing (NIPT) is a blood test that screens for chromosomal conditions during pregnancy. On the NHS in England, NIPT was added to the Fetal Anomaly Screening Programme in 2021. It is offered as a more accurate second screening test to people whose first screening test (the combined or quadruple test) shows a higher chance of one of the conditions screened for. The test analyses tiny fragments of DNA circulating in your blood to assess the chance of conditions like Down’s syndrome, Edwards’ syndrome, and Patau syndrome.

Unlike older screening methods that combine blood markers and ultrasound measurements, NIPT directly examines genetic material. It’s called ‘non-invasive’ because it uses a blood sample from your arm rather than sampling from inside the womb, which carries a small risk of miscarriage.

What NIPT actually measures

When you’re pregnant, small fragments of DNA from the placenta circulate in your bloodstream. These fragments are called ‘cell-free DNA’ (cfDNA). Most of this DNA matches the baby’s genetic makeup, though it comes from placental cells rather than the baby directly.

NIPT works by:

• Taking a blood sample from your arm (usually from 10 weeks of pregnancy onwards)
• Extracting the cell-free DNA from the plasma portion of your blood
• Sequencing millions of DNA fragments to count how many come from each chromosome
• Comparing the counts to expected patterns - extra copies of certain chromosomes indicate a higher chance of specific conditions

The test doesn’t examine every gene. It focuses on counting chromosomes to detect when there are too many or too few copies (called ‘aneuploidy’). Humans typically have 23 pairs of chromosomes. Having three copies instead of two causes the conditions NIPT screens for.

What conditions can NIPT detect?

The NHS NIPT programme screens for three main chromosomal conditions:

• Down’s syndrome (trisomy 21) - an extra copy of chromosome 21, causing learning disability and characteristic physical features
• Edwards’ syndrome (trisomy 18) - an extra copy of chromosome 18, usually causing severe disability; many babies with Edwards’ syndrome do not survive pregnancy or die shortly after birth
• Patau syndrome (trisomy 13) - an extra copy of chromosome 13, also causing severe disability with low survival rates

Some private NIPT tests screen for additional conditions, including:

• Sex chromosome aneuploidies - extra or missing X or Y chromosomes, such as Turner syndrome (missing an X chromosome in girls) or Klinefelter syndrome (an extra X chromosome in boys)
• Microdeletions - small missing pieces of chromosomes, such as 22q11.2 deletion syndrome (DiGeorge syndrome) or 1p36 deletion syndrome
• Fetal sex determination - identifying whether the baby is male or female

The NHS programme focuses on the three trisomies because they are among the most common chromosomal conditions and have well-understood health implications that allow parents to make informed decisions about continuing the pregnancy or preparing for a baby’s needs.

How accurate is NIPT?

NIPT is highly accurate for detecting Down’s syndrome. A large meta-analysis of cfDNA screening studies reported a detection rate of around 99% for Down’s syndrome in singleton pregnancies, with a false-positive rate below 0.1%. Importantly, a high-chance result is not the same as a diagnosis: how likely it is that the baby actually has the condition (the positive predictive value) also depends on your background chance, which is why a high-chance result always needs confirming with a diagnostic test.

For Edwards’ syndrome and Patau syndrome, the same meta-analysis reported detection rates of roughly 98% and 99% respectively, although the estimates for these rarer conditions are based on smaller numbers and are therefore less precise.

Important limitations to understand:

• NIPT is a screening test, not a diagnostic test. A high-chance result doesn’t confirm the baby has the condition - it means further testing is recommended.
• Sometimes the test cannot give a result (called a ‘no-call’), usually because there isn’t enough fetal DNA in the sample. Studies suggest this happens in a small percentage of cases (commonly reported as around 1–5%) and is more common earlier in pregnancy or in women with higher body weight.
• The test examines placental DNA, not the baby directly. In a small number of cases, the placenta has chromosomal differences that don’t match the baby (confined placental mosaicism), which can lead to a result that doesn’t reflect the baby’s chromosomes.
• NIPT does not screen for all genetic conditions. It won’t detect single-gene disorders (like cystic fibrosis or sickle cell disease), neural tube defects (like spina bifida), or structural abnormalities visible on ultrasound.

What happens after an NIPT result

If your NIPT shows a low chance of the conditions tested, no further action is usually needed for those specific chromosomes. You’ll continue with routine antenatal care, including the 20-week anomaly scan.

If your NIPT shows a high chance of a chromosomal condition:

• You’ll be offered an appointment with a specialist midwife or fetal medicine consultant to discuss what the result means
• Diagnostic testing will be offered - this means amniocentesis or chorionic villus sampling (CVS), which take cells directly from the pregnancy to examine the baby’s chromosomes with very high accuracy
• You have time to decide whether you want diagnostic testing, and what you might choose to do if the diagnosis is confirmed
• Support is available from specialist teams, charities, and support groups for families affected by chromosomal conditions

Diagnostic tests carry a small risk of miscarriage, which is why NIPT is offered first to those with a higher-chance result - it helps identify who would benefit from diagnostic testing while avoiding unnecessary risk for most pregnancies.

The difference between screening and diagnosis

This distinction is crucial:

• Screening tests (like NIPT) assess the chance or probability of a condition. They are not perfect and can sometimes be wrong.
• Diagnostic tests (like amniocentesis) examine the baby’s actual chromosomes and give a definitive yes-or-no answer.

NIPT cannot diagnose a condition. Even a high-chance result needs to be confirmed with a diagnostic test before any decisions about the pregnancy are made. Equally, a low-chance result doesn’t guarantee the baby doesn’t have other genetic or structural differences - it only addresses the specific chromosomes tested.

What you can do at Jeen

Jeen offers expanded NIPT screening (PrenatalSafe) that goes beyond the NHS standard panel. In addition to screening for Down’s, Edwards’, and Patau syndromes, the test includes analysis of sex chromosome aneuploidies and selected microdeletion syndromes like 22q11.2 deletion and 1p36 deletion. Blood collection is available from 10 weeks of pregnancy. It is not included in the test price: you can arrange your own draw at no extra cost, use one of our partner collection points (+£40), or book a home-nurse visit (+£65). Results are typically returned within 7-10 working days from when your sample reaches the laboratory. A genetic counsellor is available to discuss your results and what they mean for your pregnancy.