[Doctor's Explanation] What Can NIPT Tell You?

Last rewritten: December 10, 2025

This article, supervised by a physician, explains in detail the chromosomal abnormalities NIPT can detect (Trisomy 21, 18, and 13, sex chromosome abnormalities, and microdeletion syndromes), along with their detection accuracy and the limitations of NIPT as a screening test.

From the moment pregnancy is confirmed, worries such as "Is my baby growing healthily?" and "Could there be a genetic disorder?" naturally arise for many expectant mothers. With the range of prenatal testing options expanding, one test that has drawn particular attention is NIPT (Non-Invasive Prenatal Testing). NIPT can assess the state of a baby's chromosomes with high accuracy from a simple maternal blood draw, and since its introduction as clinical research in Japan in 2013, it has spread rapidly. [ref:1]

Unlike conventional amniocentesis or chorionic villus sampling, NIPT does not require inserting a needle into the uterus, so it carries almost no risk of miscarriage. It can be performed from around 10 weeks of pregnancy, with results available in about 1–2 weeks. Being able to learn about chromosomal abnormality risk at an early stage provides great reassurance for expectant mothers and their families.

However, NIPT is not an all-powerful test. Accurately understanding what it can and cannot reveal is extremely important when deciding whether to undergo testing and when interpreting the results. NIPT is a "screening test," and a positive result does not necessarily mean the fetus has an abnormality. On the other hand, a negative result does not guarantee 100% reassurance either. This article explains, from a physician's perspective, what NIPT can detect and its limitations in an easy-to-understand way.

What Is NIPT? — The Basics of the New Prenatal Test Done via Maternal Blood Draw

The full name of NIPT is "Non-Invasive Prenatal Testing." It estimates the risk of fetal chromosomal abnormalities by analyzing cell-free fetal DNA (cffDNA) contained in the mother's blood. cffDNA is released into the maternal bloodstream mainly when placental chorionic villus cells break down, and its concentration increases as pregnancy progresses. [ref:2]

Amniocentesis and chorionic villus sampling, which have long been widely used as conventional prenatal tests, are called "definitive tests" and can diagnose chromosomal abnormalities with very high accuracy. However, because these tests involve inserting a needle into the uterus to collect a sample, they carry a miscarriage risk of about 0.1–0.3%. NIPT does not require such invasive procedures — testing is completed simply by drawing blood from the mother — making it possible to obtain highly accurate information while avoiding the risk of miscarriage. This is its greatest advantage. [ref:3]

The NIPT testing process is as follows.

1. Blood is drawn at a medical institution or testing facility from 10 weeks of pregnancy onward
2. cffDNA is extracted from the collected blood and analyzed using next-generation sequencing (NGS) or similar methods
3. Based on the analysis, the presence or absence of numerical abnormalities in the target chromosomes is determined
4. Results are reported after about 1–2 weeks (positive, negative, or inconclusive)
5. If positive, a definitive test such as amniocentesis is considered

Major Chromosomal Abnormalities Detectable by NIPT

By analyzing fetal-derived DNA (cell-free fetal DNA: cffDNA) in maternal blood, NIPT can detect specific chromosomal abnormalities with high accuracy. The conditions tested fall broadly into three categories: autosomal abnormalities, sex chromosome abnormalities, and microdeletion syndromes.

Autosomal Abnormalities

The basic NIPT panel detects three autosomal trisomies: Trisomy 21 (Down syndrome), Trisomy 18 (Edwards syndrome), and Trisomy 13 (Patau syndrome). Trisomy refers to a condition in which a chromosome that is normally present in two copies exists in three copies instead.

The sensitivity of NIPT for Trisomy 21 (the probability of correctly detecting a positive case) is reported to be over 99%, and its specificity (the probability of correctly identifying a negative case) is also over 99%. For Trisomy 18 and Trisomy 13 as well, sensitivity is reported at over 95% and specificity at over 99%, both showing high accuracy. [ref:4] [ref:7]

Each of these chromosomal abnormalities is associated with distinctive physical and developmental characteristics.

• Trisomy 21 (Down syndrome): The most common of the three, occurring in about 1 in 700–1,000 births. Intellectual developmental delay and congenital heart disease may be present, but with appropriate support many individuals go on to live full social lives.
• Trisomy 18 (Edwards syndrome): Occurs in about 1 in 3,500–8,500 births. It involves severe developmental delay and structural abnormalities in multiple organs, and in many cases life-threatening complications appear soon after birth.
• Trisomy 13 (Patau syndrome): Occurs in about 1 in 5,000–20,000 births. It often involves severe intellectual disability along with structural abnormalities such as cleft lip and palate and polydactyly, and the prognosis is generally considered poor.

It is known that the incidence of these trisomies increases with advancing maternal age. In particular, among pregnant women aged 35 and older, the incidence of Trisomy 21 rises significantly, which is why many in this group consider undergoing NIPT.

Sex Chromosome Abnormalities

NIPT can also detect numerical abnormalities in the sex chromosomes (X and Y). Major conditions include Turner syndrome (45,X), Klinefelter syndrome (47,XXY), Triple X syndrome (47,XXX), and XYY syndrome (47,XYY).

The detection accuracy for sex chromosome abnormalities is somewhat lower than for autosomal trisomies, with sensitivity reported at around 90–95%. This is because these results are more susceptible to placental mosaicism (a condition in which the chromosomal makeup differs between the placenta and the fetus). In particular, detection of Turner syndrome tends to show a higher false-positive rate. [ref:5]

Sex chromosome abnormalities generally cause milder symptoms compared with autosomal abnormalities, and many affected individuals show typical development. However, they can be accompanied by infertility or learning difficulties, and early diagnosis may lead to appropriate support.

Note that in the course of analyzing sex chromosomes, NIPT may also reveal the fetus's sex. Whether the sex is disclosed depends on the facility's policy and the wishes of the pregnant woman, so it is important to confirm this in advance.

\ Learn the risk of genetic conditions such as Down syndrome /

Microdeletion Syndromes

Some facilities also offer testing for microdeletion syndromes, which arise when part of a chromosome is deleted. Representative examples include 22q11.2 deletion syndrome (DiGeorge syndrome), 1p36 deletion syndrome, 5p deletion syndrome (cri-du-chat syndrome), Prader-Willi syndrome, and Angelman syndrome.

22q11.2 deletion syndrome is the most common of the microdeletion syndromes, occurring in about 1 in 4,000 people. It can present with a wide range of symptoms, including congenital heart disease, immune deficiency, cleft palate, and learning disabilities. [ref:8]

However, NIPT testing for microdeletion syndromes is known to be less accurate than testing for autosomal trisomies. Sensitivity generally ranges from about 60–90% (varying by report), and the false-positive rate is also higher. This is because the chromosomal regions being detected are small, making the analysis more technically challenging. [ref:6]

Most microdeletion syndromes occur sporadically and show no clear correlation with maternal age, so they can occur even in younger pregnant women. If a positive result for a microdeletion syndrome is obtained via NIPT, a definitive test such as chromosomal microarray analysis or FISH testing is strongly recommended.

\ Also learn the risk of microdeletion syndromes /

What NIPT Cannot Tell You — Its Limitations

NIPT is an excellent test, but it is important to understand that it has several significant limitations. Receiving results without knowing these limitations can lead to unnecessary anxiety or false reassurance.

Not a Definitive Diagnosis

NIPT is strictly a "screening test," not a "definitive diagnosis." Even if a positive result is returned, it does not necessarily mean the fetus has a chromosomal abnormality. In cases of "placental mosaicism," where the chromosomal makeup of the placenta differs from that of the fetus, the NIPT result may not match the fetus's actual condition.

The positive predictive value (PPV) of NIPT — the probability that an abnormality is actually present given a positive result — varies greatly depending on the condition being tested for and the mother's age. For example, the PPV for Trisomy 21 in women aged 35 and older is high, at 80–90% or more, but for younger pregnant women or conditions with a lower prevalence, the PPV can fall below 50%. [ref:4]

For this reason, if NIPT returns a positive result, undergoing a definitive test such as amniocentesis or chorionic villus sampling is recommended. Making decisions about continuing or ending a pregnancy based on NIPT results alone is considered inappropriate, both medically and ethically. [ref:2]

Not All Chromosomal Abnormalities Can Be Detected

NIPT targets specific chromosomal abnormalities and cannot comprehensively test for every chromosomal or genetic disorder. For example, the following conditions are outside the scope of NIPT detection.

• Structural chromosomal abnormalities: translocations (part of a chromosome moving to another chromosome), inversions (part of a chromosome being reversed), etc.
• Single-gene disorders: hemophilia, cystic fibrosis, muscular dystrophy, etc.
• Fetal structural abnormalities: heart defects, neural tube defects, limb malformations, etc.
• Multifactorial genetic conditions: autism spectrum disorder, some forms of congenital heart disease, etc.

Fetal structural abnormalities (such as heart defects or neural tube defects) also cannot be assessed by NIPT. These require imaging diagnostics such as ultrasound. Therefore, even with a negative NIPT result, the ultrasound examinations and maternal serum marker tests normally performed during prenatal checkups cannot be omitted. [ref:9]

Factors Affecting Test Accuracy

The accuracy of NIPT is influenced by various factors, including maternal weight, gestational age, and placental condition.

• When maternal obesity is high: an increase in maternal blood volume can lower the relative concentration of cffDNA, reducing detection accuracy
• In twin pregnancies: DNA from two fetuses is mixed together, making analysis more complex
• When gestational age is early: if cffDNA concentration has not risen sufficiently, accurate results may not be obtained
• When the mother herself has a chromosomal abnormality: maternal chromosomal mosaicism or tumor-derived DNA can affect test results

In rare cases, the test may return an inconclusive result, requiring a second blood draw. This can occur when the fetal-derived DNA concentration is insufficient (low fetal fraction), among other reasons.

Points to Know Before Undergoing NIPT

For expectant mothers and families considering NIPT, here are some key points to understand beforehand.

Summary

NIPT is a groundbreaking test that can detect fetal chromosomal abnormalities from maternal blood with high accuracy. It shows a very high detection rate for the major autosomal trisomies — Trisomy 21, Trisomy 18, and Trisomy 13 — and offers the major advantage of being available from an early stage without the risk of miscarriage. Furthermore, by extending the scope of testing to sex chromosome abnormalities and microdeletion syndromes, it enables more comprehensive screening.

At the same time, it is important to understand that NIPT is a screening test, not a definitive diagnosis, and that it cannot detect every chromosomal abnormality or congenital condition. If a positive result is obtained, it is important to undergo a definitive test to confirm an accurate diagnosis. Also, even with a negative result, it is recommended to continue attending regular prenatal checkups (such as ultrasound examinations) without skipping them.

Whether to undergo NIPT and which test items to choose should be decided carefully in consultation with your doctor or a genetic counselor. Once you fully understand the significance and limitations of the test, we hope you are able to make the choice that is best for you and your family. NIPT is a first step toward "knowing," and by combining it with the definitive tests and medical support that follow, you can create an environment where you can approach childbirth with peace of mind.

\ Learn the genetic disease risk for your baby /

Frequently Asked Questions

Q1. From how many weeks of pregnancy can NIPT be taken?

A. NIPT is generally available from 10 weeks of pregnancy onward. In early pregnancy, the concentration of fetal-derived cell-free DNA (cffDNA) has not yet risen sufficiently, so accurate results may not be obtainable before 10 weeks. Since results are reported about 1–2 weeks after the blood draw, you can learn about chromosomal abnormality risk at an early stage of pregnancy.

Q2. If NIPT comes back positive, does that mean the baby definitely has an abnormality?

A. A positive NIPT result does not necessarily mean the fetus has a chromosomal abnormality. NIPT is a screening test, and false positives can occur due to factors such as placental mosaicism. Because the positive predictive value varies depending on the condition and maternal age, it is recommended that a definitive test such as amniocentesis always be performed following a positive result.

Q3. Can I feel reassured if NIPT comes back negative?

A. The negative predictive value of NIPT is extremely high (over 99.9% for Trisomy 21 in particular), so a negative result means the likelihood of the tested chromosomal abnormalities being present is very low. However, NIPT cannot assess chromosomal abnormalities, genetic disorders, or structural abnormalities outside its testing scope. Therefore, even with a negative result, it is important to continue attending regular prenatal checkups (such as ultrasound examinations).

Q4. How is NIPT different from amniocentesis?

A. NIPT is a non-invasive screening test performed using only a maternal blood draw, carrying almost no risk of miscarriage. Amniocentesis, on the other hand, is an invasive definitive test that involves inserting a needle into the uterus to collect amniotic fluid, carrying a miscarriage risk of about 0.1–0.3%, but it can definitively diagnose chromosomal abnormalities. It is common practice to perform amniocentesis as confirmation when NIPT returns a positive result.

Q5. Can NIPT be taken for a twin pregnancy?

A. It is possible to undergo NIPT even in a twin pregnancy. However, in the case of dizygotic (fraternal) twins, DNA from both fetuses is mixed together, which can make it difficult to determine whether an abnormality is present in only one of them. Detection accuracy may also be somewhat lower compared with a singleton pregnancy, so results should be interpreted with caution. We recommend consulting thoroughly with your doctor beforehand.

Q6. Should I also undergo testing for microdeletion syndromes?

A. Testing for microdeletion syndromes is characterized by lower accuracy compared with testing for autosomal trisomies. However, since some conditions, such as 22q11.2 deletion syndrome, occur at a certain frequency regardless of maternal age, it may be worth considering for those who wish for broader screening. We recommend making this decision in consultation with your doctor, after fully understanding the accuracy of the test and the risk of false positives.

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