[Doctor's Explanation] What's the Difference Between NIPT and Preimplantation Genetic Testing? ~Why "NIPT" and "Preimplantation Genetic Testing" Are Easily Confused~

Rewritten on: March 4, 2026

NIPT is a non-invasive screening test that evaluates the risk of fetal chromosomal abnormalities from maternal blood during pregnancy, while preimplantation genetic testing (PGT) examines the genetic information of embryos obtained through IVF before pregnancy. This article explains in detail the differences between the two and how to choose between them.

When pregnancy is confirmed, many people feel anxious, wondering "Is the baby growing well?" or "Could there be any abnormalities?" In recent years, NIPT (Non-Invasive Prenatal Testing) has become widely known as a prenatal test that addresses such concerns.
At the same time, many people encounter the term "preimplantation genetic testing" and are unsure how it differs from NIPT. However, this question is actually based on a misunderstanding. Because the names sound similar, NIPT and preimplantation genetic testing are often assumed to belong to the same category of tests, but there is a decisive difference: one is a "test performed after pregnancy" and the other is a "test performed before pregnancy."
This difference in timing is the most important point when choosing between tests. This article explains, from a specialist perspective, the characteristics of NIPT and preimplantation genetic testing and how to decide which to use. We hope that accurate information about genetic medicine will help you and your family find the best option for your situation.

What Is NIPT?

― A "non-invasive screening test" performed during pregnancy ―
NIPT is a test that can evaluate the risk of fetal chromosomal abnormalities simply by drawing a sample of the mother's blood during pregnancy. Its formal name is "Non-Invasive Prenatal Testing," and it can be performed from the 10th week of pregnancy onward. By analyzing the trace amounts of fetal-derived DNA fragments (cell-free DNA, or cfDNA) contained in maternal blood using advanced technologies such as next-generation sequencing (NGS), the test estimates with high accuracy whether the fetus has a chromosomal abnormality.

The greatest feature of this test is that it is "non-invasive." Conventional confirmatory tests such as amniocentesis and chorionic villus sampling require inserting a needle into the uterus to obtain a sample, and have been reported to carry a miscarriage risk of approximately 0.1–0.3%. Because NIPT requires only a blood draw, it is a test that carries almost no risk of miscarriage and places extremely little physical burden on the pregnant woman.[ref:1][ref:2]

Since NIPT was introduced into clinical practice, it has spread rapidly around the world. In 2020, the American College of Obstetricians and Gynecologists (ACOG) issued guidelines recommending that information about NIPT be provided to all pregnant women, regardless of age.[ref:6] This reflects the high detection accuracy and low invasiveness of NIPT, and has established it internationally as a standard option for prenatal screening.

NIPT's Test Accuracy and Target Conditions

The basic screening items in NIPT detect three chromosomal abnormalities with high accuracy: trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). In particular, the sensitivity for trisomy 21 (Down syndrome) is said to be over 99%, and international research has shown that the false-positive rate is also very low.[ref:7]

In recent years, depending on the testing facility, it has also become possible to check for sex chromosome abnormalities (such as Turner syndrome and Klinefelter syndrome) and microdeletion syndromes (such as 22q11.2 deletion syndrome). However, the detection accuracy for these additional test items may differ somewhat from that of the three basic conditions, so it is important to confirm details with the testing facility in advance.

Note that NIPT is strictly a "screening test" and does not provide a definitive diagnosis. If a high-risk result is returned, an invasive confirmatory test such as amniocentesis is required to establish a definitive diagnosis. Conversely, even if the result is "low risk," there remains a small possibility of a false negative (a case where an abnormality actually exists but is missed). Causes of false positives and false negatives include an insufficient ratio of maternal to fetal-derived cfDNA (the fetal fraction) and confined placental mosaicism.[ref:3]

The general process for undergoing NIPT is as follows.

1. Receive genetic counseling to understand the content, significance, and limitations of the test
2. After the 10th week of pregnancy, approximately 10–20 mL of blood is drawn from the mother
3. Fetal-derived cfDNA in the blood is analyzed to assess the risk of chromosomal abnormality
4. Results are usually available within 1–2 weeks and are reported as "low risk" or "high risk"
5. If high risk, additional confirmatory tests such as amniocentesis are considered for a definitive diagnosis

The History and Technical Background of NIPT

The foundation of NIPT was laid by research in 1997, when Professor Dennis Lo and colleagues at the Chinese University of Hong Kong discovered that fetal-derived cell-free DNA exists in maternal plasma.[ref:8] This groundbreaking discovery opened the way to non-invasively analyzing a fetus's genetic information from the mother's blood. With the subsequent rapid development of next-generation sequencing (NGS) technology, commercial NIPT began to be introduced into clinical practice around 2011.

In Japan, NIPT began as clinical research in 2013 under a certification system established by the Japan Medical Association. Initially it was offered only at a limited number of accredited facilities, but as awareness of the test grew, it also became widely available at non-accredited facilities, and today an increasing number of pregnant women have access to NIPT as an option. However, because accredited and non-accredited facilities may differ in the level of genetic counseling and follow-up support they provide, it is recommended to choose a facility carefully.

What Is Preimplantation Genetic Testing (PGT)?

― A genetic test performed "before" pregnancy ―
Preimplantation Genetic Testing (PGT) is a test that examines the genetic information of a fertilized egg (embryo) obtained through in vitro fertilization (IVF) before it is transferred into the uterus. The fact that it is performed before pregnancy is established is the fundamental difference from NIPT, which is performed after pregnancy.

In PGT, a few cells are taken from the trophectoderm (the portion that will later become the placenta) of an embryo that has developed to the blastocyst stage (approximately day 5–6 after fertilization), and these cells are analyzed for chromosomal abnormalities or specific genetic disorders. Trophectoderm biopsy technique has advanced year by year, making it possible to collect a sufficient number of cells while minimizing damage to the embryo. Based on the results, an embryo without genetic abnormalities can be selected for transfer into the uterus, potentially reducing the risk of a child being born with a genetic disorder.

Because IVF is a prerequisite for undergoing preimplantation genetic testing, it cannot be performed with a naturally conceived pregnancy. This is one major difference from NIPT, which can be performed after pregnancy regardless of whether conception was natural or via IVF. IVF involves physical burdens such as ovulation induction and egg retrieval, as well as substantial financial costs, so it is important to understand these overall burdens beforehand when considering PGT.[ref:4]

The Three Types of PGT (PGT-A, PGT-SR, PGT-M)

PGT is classified into the following three types depending on the purpose of the test. Since the target population and purpose differ for each, it is important to understand them correctly.

The Issue of Mosaic Embryos in PGT

One clinically important issue when performing PGT is how to handle "mosaic embryos." A mosaic embryo is one in which cells with a normal chromosome number and cells with an abnormal chromosome number coexist within the same embryo. In PGT, a few cells are taken from the trophectoderm of the blastocyst for analysis, but these sampled cells do not necessarily fully reflect the genetic makeup of the entire embryo.

For example, cases have been reported in which chromosomal aneuploidy was detected in the trophectoderm, yet the inner cell mass (ICM), which will become the fetus, had a normal chromosomal composition. Such localized mosaicism is one factor that complicates the interpretation of PGT results. International guidelines state that, under certain conditions, transfer may be considered even for embryos in which a low level of mosaicism is detected, but such decisions require advanced genetic knowledge and careful counseling.[ref:6]

This issue of mosaic embryos is also one reason why some patients choose to undergo NIPT in addition after PGT. Even when an embryo is transferred after being judged "normal" by PGT, the possibility of mosaicism cannot be completely ruled out, so undergoing NIPT after pregnancy is established allows for more comprehensive screening of chromosomal abnormalities.

How Should You Choose Between NIPT and Preimplantation Genetic Testing?

― How to think about choosing a test ―
Because NIPT and PGT differ greatly in the timing and purpose of testing, which one is appropriate depends on each couple's individual circumstances. Below is a summary of the situations in which each test is suitable.

NIPT is a test chosen after pregnancy has been established, whether naturally or through IVF, when you want to know the risk of fetal chromosomal abnormality. Its major advantage is that it allows screening with minimal burden on the mother, particularly in cases of advanced maternal age (35 or older) or when an abnormality is suspected on ultrasound. The purpose of the test is simply to "obtain information," which can then serve as material for considering the course of the pregnancy and future options.

On the other hand, PGT is considered when a specific genetic disease risk is already known, or when recurrent miscarriage has been experienced, and the couple wants to select a genetically normal embryo before pregnancy is established. While it has the distinctive feature of allowing intervention before pregnancy, it also involves aspects related to the selection of life and is a test accompanied by ethical and social debate.

In terms of cost, NIPT is also more accessible than PGT, generally costing around 100,000–200,000 yen, whereas PGT adds the cost of genetic testing on top of IVF costs, meaning the total can range from several hundred thousand yen to over one million yen. This difference in financial burden is also an important consideration when choosing between the tests.

Situations in which NIPT is particularly considered can be summarized as follows.

• Wanting to know the risk of fetal chromosomal abnormality after natural conception
• Advanced maternal age (35 or older) and concerned about risks such as Down syndrome
• A concerning finding was observed on an ultrasound examination
• Wanting to undergo screening first, before amniocentesis or chorionic villus sampling
• Wanting to obtain information through a method with no risk of miscarriage
• Wanting additional reassurance after undergoing PGT with IVF

Comparison Chart of NIPT and Preimplantation Genetic Testing

The table below summarizes the differences between the two tests. It should help clarify how fundamentally different the two tests are in nature.

As the table above shows, NIPT is a test to "obtain information about a baby that already exists in the womb," while PGT is a test to "select an embryo before transfer." Because the two tests are fundamentally different in nature, it is important to understand that this is not a question of "which is superior" but rather that "each is useful in different situations."

Things to Consider Before Undergoing Testing

Neither test is something you "must" undergo — each is simply one option among several. It is most important to receive sufficient information about the significance and limitations of the test, make use of genetic counseling as needed, and make a choice that both partners are satisfied with.

Genetic counseling provides not only a technical explanation of the test, but also an opportunity to think together with a specialist about what options exist after results are received and how to process those results emotionally. In particular, because PGT is premised on IVF, it carries a significant physical, financial, and psychological burden, and it is important to gather sufficient information and prepare emotionally before undergoing the test.

Also, even if an NIPT result comes back "high risk," it must be remembered that this is merely a probabilistic assessment, not a definitive diagnosis. Whether to undergo a confirmatory test, and how to respond to its results, should be carefully decided based on the couple's own values and life plans. Healthcare providers are there to provide information and support, and the final decision rests with the individual and their family.

Before undergoing testing, it is recommended that couples discuss questions such as: "What do we want to learn from this test?" "What action would we want to take if the result is positive?" and "Is not undergoing testing also an option for us?" Organizing your thoughts in advance in this way will help you make a calm and proactive decision once results are received.

The Role and Importance of Genetic Counseling

When considering NIPT or preimplantation genetic testing, genetic counseling plays an extremely important role both before and after the test. Genetic counseling is a process in which a board-certified clinical geneticist or certified genetic counselor provides accurate medical information and psychosocial support to individuals and families who have concerns or questions about genetics.

In pre-test counseling, you can receive detailed explanations of how NIPT and PGT each work, which conditions can and cannot be detected, the meaning of sensitivity and specificity, the possibility of false positives and false negatives, and the options available once results are obtained. Because NIPT in particular is a screening test, it is important to correctly understand that a "high risk" result does not necessarily mean a disease is present — this understanding helps reduce psychological distress after receiving results.

In post-test counseling, in addition to receiving a careful explanation of how to interpret the results from a specialist, couples are given the opportunity to think together about the path forward based on the results, while their own wishes are respected. The Japan Society of Human Genetics and the Japanese Society for Genetic Counseling recommend that genetic counseling be received at every stage involved in prenatal testing. At the seeDNA Institute of Genetic Medicine, our specialist staff are also happy to carefully support you with any concerns or questions about testing, so please feel free to contact us.

Understanding the Differences Between These Tests Is the First Step Toward a Confident Choice

NIPT is a non-invasive screening test that evaluates the risk of fetal chromosomal abnormality from maternal blood during pregnancy, while preimplantation genetic testing (PGT) is a genetic test performed on embryos obtained through IVF before pregnancy. We hope it is now clear that these tests differ completely in timing, method, and purpose.

NIPT is intended for "those who are already pregnant" and offers an easy way to assess risk through a simple blood draw, though it has the limitation of not being a definitive diagnosis. PGT is intended for "those who are trying to become pregnant" who have a specific genetic risk or a history of recurrent pregnancy loss, and it involves the major step of undergoing IVF.

Whichever test you choose — or even the choice not to undergo testing at all — it is important to make your decision based on accurate knowledge. Each test has its own advantages and disadvantages, and ethical aspects must also be considered. In recent years, information about prenatal testing has flooded the internet, but some of it is inaccurate. Consulting a trusted medical institution or specialist and obtaining evidence-based information will lead to a choice you won't regret.

The field of genetic medicine is advancing daily, and the range of conditions detectable by NIPT is likely to expand further in the future. Likewise, advances in analytical technology are moving PGT toward more accurate and safer testing. While keeping an eye on these technological developments, we hope you will always keep in mind the question, "What information do we truly need?" when deciding whether to undergo testing.

We hope this article helps you and your family find the best choice for your situation.

\Find out your risk for Down syndrome and sex chromosome conditions/

Learn more about Non-Invasive Prenatal Testing (NIPT)

Apply / Purchase a Kit

Frequently Asked Questions

Q1. What is the biggest difference between NIPT and preimplantation genetic testing?

A. The biggest difference is "when the test is performed." NIPT is a screening test performed by drawing maternal blood from the 10th week of pregnancy onward, after pregnancy has already been established. Preimplantation genetic testing (PGT), on the other hand, is a method of genetically testing a fertilized egg (embryo) obtained through IVF before it is transferred into the uterus. In other words, NIPT is performed "after pregnancy" and PGT is performed "before pregnancy" — they are fundamentally different in nature.

Q2. If an abnormality is found on NIPT, does that mean an immediate definitive diagnosis?

A. No. NIPT is strictly a screening test and is not a definitive diagnosis. Even when NIPT returns a "high risk" result, there are cases where no abnormality is actually present (false positives). Therefore, if a high-risk result is returned, a confirmatory test such as amniocentesis or chorionic villus sampling is needed to establish a final diagnosis. We recommend consulting a specialist through genetic counseling regarding how to interpret the results.

Q3. Can anyone undergo preimplantation genetic testing (PGT)?

A. No, preimplantation genetic testing is not something anyone can freely undergo. Because PGT is premised on IVF, assisted reproductive technology (ART) must first be undertaken. In addition, in Japan, PGT-A is intended for couples with a history of recurrent implantation failure or recurrent miscarriage, and PGT-M is intended for serious genetic disorders and requires an individual application and review by the Japan Society of Obstetrics and Gynecology. If you are considering the test, please first consult a specialized medical institution.

Q4. Where can I get NIPT, and what does it typically cost?

A. NIPT is available both at accredited facilities (certified by the Japan Medical Association Federation) and at non-accredited medical institutions. Costs vary depending on the facility and test items, but generally range from about 100,000 to 200,000 yen. Accredited facilities often include genetic counseling as part of the process, which is an advantage in terms of pre- and post-test support. The seeDNA Institute of Genetic Medicine also offers NIPT, so please check our official page for details.

Q5. Do people ever undergo both NIPT and preimplantation genetic testing?

A. Yes, depending on the situation, some people undergo both tests. For example, some people choose to undergo NIPT after pregnancy is established, having already had an embryo transferred following a PGT-A result confirming a normal chromosome number. Because PGT analyzes cells from the embryo's trophectoderm, it does not necessarily reflect 100% of the genetic information of the entire embryo (due to phenomena such as mosaicism). For this reason, some people choose to also use NIPT for additional reassurance. However, whether both tests are necessary varies by individual situation, so please consult closely with your doctor.

Q6. Is genetic counseling mandatory?

A. While it is not a legal requirement, genetic counseling is strongly recommended when undergoing NIPT or preimplantation genetic testing. In particular, at NIPT facilities accredited by the Japan Medical Association Federation, pre-test genetic counseling is mandatory. In genetic counseling, you can obtain important information from specialists — such as the accuracy and limitations of the test, the options available once results are received, and psychological support — that you should know before undergoing testing. We recommend making active use of it in order to correctly understand your results and make a decision you won't regret.

Q7. Can NIPT reveal the sex of the baby?

A. Because NIPT can analyze sex chromosomes (X and Y chromosomes), it may be possible to learn the sex of the fetus from the test results in some cases. However, whether sex is disclosed depends on the testing facility and testing plan. In addition, at facilities accredited by the Japan Medical Association Federation, disclosure of information regarding sex chromosomes may, in principle, be handled with caution. Undergoing NIPT for the purpose of confirming the baby's sex is not recommended; the test is fundamentally intended to be undergone for medical purposes.

Reassuring Support from the seeDNA Institute of Genetic Medicine

The seeDNA Institute of Genetic Medicine is a trusted specialist institution for DNA testing and genetic testing, certified under the international quality standard ISO9001 and the Privacy Mark for personal information protection.
If you have concerns about family or parent-child biological relationships, or a partner's infidelity, our DNA testing specialists are here to provide reassuring support, so please feel free to contact us.

[Free Consultation with Specialist Staff]

If you have any questions,
please feel free to contact our toll-free number.

0120-919-097

\Open every day, including weekends/
Business hours: Monday–Sunday 9:00 AM–6:00 PM
(excluding holidays)

Author

M.D., Ph.D.
Tasuku Hiroshige

Ph.D. in Medicine; Board-certified specialist and instructor of the Japanese Urological Association; Board-certified physician of the Japanese Society of Medical Oncology; Board-certified specialist of the Japanese Society of Anti-Aging Medicine; Occupational physician certified by the Japan Medical Association; Board-certified physician of the Japanese Society of Chemotherapy; Board-certified physician of the Japanese Society for Sexually Transmitted Infections; Certificate of da Vinci System Training As a Console Surgeon, and more.
After graduating from Kagoshima University School of Medicine in 2010, he built extensive clinical experience as a urologist. In addition to his clinical work, he is also actively engaged in academic activities such as conference presentations, writing papers, and securing research funding. He holds specialist qualifications across a wide range of fields, including urology, cancer treatment, anti-aging medicine, and infectious disease treatment. Drawing on his extensive medical knowledge and skills, he provides care tailored to each individual patient.

[References]

(1) Japan Society of Obstetrics and Gynecology, August 2022
(2) Med J Aust, July 2015
(3) J Plast Reconstr Aesthet Surg, March 2021
(4) Diagn Cytopathol, February 2016
(5) Japan Society of Obstetrics and Gynecology, 2025
(6) Pediatr Surg Int, 1997
(7) Igenomix Japan, July 2022
(8) Hara Medical Clinic | Fertility Treatment & IVF in the Shinjuku/Shibuya Area