[Expert Explanation] The Background of a Positive NIPT Result and the Need for Diagnostic Confirmation

Rewritten on: November 1, 2025

Our experts explain in detail the differences, risks, and selection criteria for the diagnostic confirmation tests (chorionic villus sampling, amniocentesis, and microarray analysis) required after receiving a positive NIPT result.

Non-invasive prenatal genetic testing (NIPT) analyzes fetal-derived cell-free DNA (cfDNA) present in maternal blood, and is a screening test that primarily assesses the likelihood of chromosomal abnormalities such as trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). Because NIPT can be performed with just a blood draw and places very little physical burden on the mother and fetus, it has spread rapidly in recent years [ref:1]. However, a "positive" result on NIPT (indicating a possible abnormality) does not mean a definitive diagnosis has been made. NIPT is ultimately a screening test, and its "positive predictive value (PPV)" varies greatly depending on the condition being tested for and the mother's age [ref:5]. In particular, for trisomy 13 and trisomy 18, the false-positive rate is known to be relatively high, so even after receiving a positive result, there are a certain number of cases where the fetus actually has no abnormality.

At this stage, the most important thing is to correctly understand the invasive diagnostic methods that lead to a confirmed diagnosis, along with their characteristics and risks, and to thoroughly discuss the situation with your attending physician or genetic counselor in order to determine the best choice for you and your family. Regarding prenatal testing, Japan's Ministry of Health, Labour and Welfare's "Expert Committee on Prenatal Testing including NIPT" has published a report [ref:1], and the Children and Families Agency also operates an information website, showing that public support systems are being put in place [ref:4].

This article organizes, with clear section headings, the differences among the diagnostic confirmation options available after a positive NIPT result (chorionic villus sampling, amniocentesis, and microarray analysis, among others) and explains them in detail. We will share evidence-based information about the advantages and disadvantages of each testing method, when they can be performed, the range of abnormalities they can detect, and their risks.

What Is a Diagnostic Confirmation Test?

The Difference Between Screening Tests and Diagnostic Confirmation

Prenatal testing is broadly divided into two categories: "screening tests" and "diagnostic confirmation (invasive testing)." Understanding the difference between these two accurately is essential when considering the next step after a positive NIPT result.

• Screening tests (sorting/filtering tests): These assess the likelihood of an abnormality and carry the possibility of false positives and false negatives. In addition to NIPT, maternal serum marker testing (quad test) and combined testing (NT measurement plus serum markers) also fall into this category. Because these tests are non-invasive, they are highly safe, but they only indicate a "probability" and cannot provide a final diagnosis.
• Diagnostic confirmation (invasive testing): These tests directly sample fetal or placental tissue to analyze chromosomes or genes, providing a more accurate assessment. Chorionic villus sampling and amniocentesis fall into this category; because the chromosomes of the collected cells are directly observed and analyzed, diagnostic accuracy is extremely high. However, since these procedures involve inserting a needle into the uterus, there is a small but real risk of miscarriage.

A positive NIPT result is only at the stage of "high likelihood," and it is only after diagnostic confirmation that an accurate diagnosis can be obtained. NIPT's sensitivity (the probability of correctly testing positive when the condition is present) is said to be extremely high, over 99%, but its specificity (the probability of correctly testing negative when the condition is absent) is also not 100%, so false positives can occur [ref:5]. Therefore, it is not medically recommended to decide whether to continue or terminate a pregnancy based solely on NIPT results; a diagnostic confirmation test must always be performed, and future plans should be considered while receiving genetic counseling [ref:6].

Methods of Diagnostic Confirmation: Explained by Type

Here we organize the representative diagnostic confirmation methods and their analysis techniques, covering their characteristics, risks, and applicable timing. Diagnostic confirmation mainly involves two types of sample collection—"chorionic villus sampling" and "amniocentesis"—and various analysis technologies such as "G-banding," "FISH," and "microarray analysis" are applied to the collected samples. Which testing method is chosen is determined by comprehensively weighing many factors, including gestational week, the capabilities of the testing facility, and the wishes of the pregnant woman and her family.

Chorionic Villus Sampling (CVS)

■ Timing and Sample Source
・Typically performed around 10 to 13 weeks of pregnancy. This is the earliest stage at which a prenatal diagnostic confirmation test can be performed, making it a strong option for families who want results early.
・The sample collected is chorionic villus tissue (part of the tissue that becomes the placenta). Because the chorionic villi originate from the same fertilized egg as the fetus, they generally carry the same genetic information as the fetus. Collection methods include the transabdominal approach (inserting a needle through the abdomen) and the transcervical approach (inserting a thin tube through the vagina), but in Japan the transabdominal approach is the mainstream method.

■ Analysis Methods and Detectable Range
・Standard chromosome analysis (G-banding, FISH, etc.) detects numerical chromosomal abnormalities (trisomies and monosomies) as well as structural abnormalities (translocations, deletions, duplications, etc.).
・Microarray analysis (CMA / SNP array) can also be used in combination, potentially detecting small deletion/duplication variants (copy number variants, or CNVs) that are difficult to detect with conventional G-banding [ref:2]. However, not all CNVs can be detected, and the detection limit varies depending on the platform and resolution used.

■ Risks and Points to Consider
・Miscarriage risk: Reports suggest approximately 0.2% for the transabdominal approach, though this varies depending on the facility and the operator's experience.
・There is a possibility of placental mosaicism in chorionic villus tissue. This is a phenomenon in which the chromosomal makeup differs between the placental tissue and the fetus itself; even if a chromosomal abnormality is detected via chorionic villus sampling, the actual fetus may have normal chromosomes. The incidence of placental mosaicism is estimated to be about 1-2%.
・While results can be obtained early, the possibility of error due to placental mosaicism and the limited number of facilities that offer this test must also be taken into account. When placental mosaicism is suspected, it may be recommended to additionally perform amniocentesis to confirm the finding.

Amniocentesis

■ Timing and Sample Source
・As a rule, this is performed from 15 weeks of pregnancy onward, because performing it before 15 weeks is associated with a higher risk of complications. It is generally performed around 15 to 18 weeks, and results typically take about 2-3 weeks.
・The sample collected consists of fetal-derived cells floating in the amniotic fluid. Under ultrasound guidance, a thin needle is inserted through the abdomen, and about 15-20 mL of amniotic fluid is aspirated. The amniotic fluid contains cells shed from the fetus's skin and digestive tract, among other sources, and these cells are cultured for chromosome analysis.

■ Analysis Methods and Detectable Range
・G-banding chromosome analysis allows all 46 chromosomes to be observed with high precision. In addition to numerical chromosomal abnormalities, it can also detect relatively large structural abnormalities (translocations, inversions, deletions, duplications, etc.).
・FISH (fluorescence in situ hybridization) can be used to rapidly screen (in about 1-2 days) for abnormalities in specific chromosomes (13, 18, 21, X, Y, etc.).
・When needed, microarray analysis can be used in combination to potentially detect small variants that might otherwise be missed by G-banding [ref:3].

■ Risks and Points to Consider
・Miscarriage/stillbirth risk: Generally reported at about 0.1-0.3%, which is somewhat lower than that of chorionic villus sampling [ref:6].
・Complications such as bleeding, induced uterine contractions, rupture of membranes, and infection can also rarely occur.
・Amniocentesis has the advantage of being less affected by placental mosaicism compared to chorionic villus sampling. Because it directly analyzes fetal-derived cells, the reliability of the results is high, making it a relatively well-balanced option in terms of both stability and accuracy.
・On the other hand, since it can only be performed from 15 weeks of pregnancy onward, results are not available until around 17-20 weeks, which can limit the time available for decision-making.

Chromosomal Microarray Analysis (CMA / SNP Array)

■ Overview and Principle
・Microarray analysis is a technique that detects copy number variants (CNVs) across the entire genome at high resolution. It has the potential to capture minute chromosomal abnormalities (microdeletions and microduplications) of a few hundred kilobases or less that are difficult to detect with conventional G-banding, contributing to improved accuracy in prenatal diagnosis [ref:2].
・When SNP arrays are used, uniparental disomy (UPD) and regions of homozygosity can also be detected, providing more detailed genetic information.
・The Japan Society of Obstetrics and Gynecology has also published "Points to Note When Using Chromosomal Microarray Testing" [ref:2], and its application and interpretation require specialized knowledge and careful handling.

■ Applications and Advantages
・It may be used to provide additional genetic information when structural abnormalities (heart malformations, brain abnormalities, limb abnormalities, etc.) are found in the fetus via ultrasound. Some reports suggest that in fetuses with ultrasound abnormalities, even when G-banding analysis shows a normal result, microarray analysis detects a clinically significant CNV in about 6% of cases.
・It may lead to the discovery of small deletion/duplication variants (e.g., 22q11.2 deletion syndrome, Williams syndrome) that cannot be detected by conventional chromosome analysis, providing useful information for predicting fetal outcomes and planning subsequent management.
・However, it should be noted that balanced rearrangements (reciprocal translocations, inversions, etc.) cannot be detected by microarray methods, since they do not cause any overall change in copy number [ref:3].

■ Challenges and Points to Consider
・There is a possibility of finding a variant of uncertain significance (VOUS). A VOUS is a variant whose clinical significance is not yet clear based on current medical knowledge, and its discovery can cause significant anxiety for the pregnant woman and her family.
・Because interpretation is highly specialized and complex, it is recommended that this be performed at a facility with a well-established genetic counseling system [ref:3].
・The number of facilities that can perform this test is often limited, and in some regions patients may need to travel to a medical institution far from home.
・When performing chromosomal microarray testing, appropriate explanation and informed consent must be obtained in accordance with the guidelines of the Japan Society of Obstetrics and Gynecology and related academic societies.

Comparison Table: Summary of Diagnostic Confirmation Methods

Below is a summary of the main features of the diagnostic confirmation methods. Please note that actual application may vary by facility and testing content, so please check with your attending physician for details.

Features of Chorionic Villus Sampling

• Timing: 10-13 weeks of pregnancy
• Sample source: Chorionic villi (placental tissue)
• Main analysis methods: G-banding, FISH, microarray
• Detectable range: Chromosome number/structural abnormalities, small CNVs
• Risk: Miscarriage risk of about 0.2%, possibility of placental mosaicism
• Advantages: Early testing and early results possible
• Disadvantages: Mosaicism-related error, limited facilities

Features of Amniocentesis

• Timing: From 15 weeks of pregnancy onward
• Sample source: Fetal-derived cells in amniotic fluid
• Main analysis methods: G-banding, FISH, microarray
• Detectable range: Chromosomal abnormalities, structural abnormalities, small variants
• Risk: Miscarriage risk of 0.1-0.3%, rupture of membranes, infection, etc.
• Advantages: Relatively good balance of accuracy and safety
• Disadvantages: Somewhat limited timing window, waiting period for results

Features of Microarray Analysis

• Timing: Uses samples from chorionic villus sampling or amniocentesis
• Sample source: Chorionic villi or amniotic fluid
• Main analysis method: Microarray (CNV detection)
• Detectable range: Small deletion/duplication variants
• Risk: Possibility of finding variants that are difficult to interpret (VOUS)
• Advantages: More precise genetic information can be obtained
• Disadvantages: VOUS interpretation is difficult, limited facilities available, cannot detect balanced rearrangements

Decision Criteria and Points to Consider When Choosing

When choosing a diagnostic confirmation test, it is important to weigh multiple factors comprehensively. Right after receiving a positive NIPT result, you may feel anxious or rushed, but it is important to first consult a trusted specialist and calmly organize the information. Below are key points to consider when choosing a diagnostic confirmation test.

1. Gestational week: The suitable test method varies depending on whether you want results early or want to reduce risk. If you are 10-13 weeks pregnant, chorionic villus sampling is an option; if you are 15 weeks or beyond, amniocentesis applies. If you are past both windows, check with your doctor about which test can be performed at your current gestational week.
2. Facility capabilities: Check in advance whether diagnostic confirmation is available and whether the facility has the equipment to perform microarray analysis. Not all obstetric facilities offer invasive testing. Since microarray analysis in particular is only available at a limited number of facilities, it is important to get a referral to a specialized facility if needed.
3. Risk tolerance: Organize your own and your partner's thoughts on how much miscarriage risk or possibility of test complications you can accept. Chorionic villus sampling carries an estimated miscarriage risk of about 0.2%, and amniocentesis about 0.1-0.3%, but how these figures are perceived varies from person to person.
4. Depth of information: Whether confirming the major numerical chromosomal abnormalities (trisomy 21, 18, 13, etc.) is sufficient, or whether you want detailed information down to small deletion/duplication variants, will affect whether you consider adding microarray analysis. However, more information is not necessarily better—you should also consider the possibility of unexpected findings, such as the discovery of a VOUS.
5. Explanation and consent: Check whether genetic counseling and a system for explanation before and after testing are in place. Because prenatal testing can involve major decisions depending on the results, it is important to receive thorough explanation and to proceed with the test only once you feel you understand and accept it. Facilities with certified genetic counselors or clinical genetics specialists on staff can provide comprehensive care, including psychological support.

In Japan, efforts are underway to establish systems for providing NIPT and prenatal testing along with the information that supports it, and guidelines and reports have been published by the Ministry of Health, Labour and Welfare and the Children and Families Agency, among others [ref:1] [ref:4]. For example, the report from the Ministry of Health, Labour and Welfare's "Expert Committee on Prenatal Testing including NIPT" describes in detail the appropriate implementation framework for NIPT and the importance of genetic counseling. In addition, the Children and Families Agency's "Prenatal Testing Information Site" provides clear, accessible information so that pregnant women and their families can obtain accurate information about prenatal testing [ref:4]. Furthermore, the Japan Association of Obstetricians and Gynecologists has also expressed views on the future development and current challenges of NIPT and prenatal testing [ref:7], and we recommend checking this kind of public information before undergoing testing.

Summary: Moving Forward with Peace of Mind

A positive NIPT result is ultimately just "a sign of possibility." Diagnostic confirmation methods include chorionic villus sampling, amniocentesis, and microarray analysis, each with its own characteristics, advantages, and risks. Chorionic villus sampling has the advantage of providing early results in the first trimester (10-13 weeks), but carries the possibility of error due to placental mosaicism. Amniocentesis offers an excellent balance of accuracy and safety, but can only be performed from 15 weeks of pregnancy onward. Microarray analysis provides more precise genetic information, but also comes with challenges such as the discovery of VOUS findings and difficulty of interpretation.

It is important to make an appropriate choice by consulting with a specialist while weighing factors such as timing, safety, accuracy, and the level of explanation and support available. Whether to undergo diagnostic confirmation after a positive NIPT result, and which testing method to choose, is an important decision that involves not only medical judgment but also your own and your family's values and outlook on life. That is precisely why we hope you will not carry this burden alone, and will make active use of genetic counseling.

When considering or undergoing testing, it is a good idea to check the following points:

• Whether a genetic counseling system is available (whether certified genetic counselors or clinical genetics specialists are on staff)
• The testing facility's track record and equipment (annual number of invasive tests performed, whether microarray analysis is available)
• Risk and time until results (the miscarriage risk of each testing method, the time required until results are available)
• Testing costs (prenatal diagnosis is in most cases not covered by insurance; chorionic villus sampling and amniocentesis typically cost around 100,000-200,000 yen, and adding microarray analysis will incur additional costs)
• Follow-up support after testing (explanation of results, psychological support, referral to specialists as needed, etc.)

We sincerely hope that, with appropriate information and expert support, you will be able to reach a decision you feel at peace with, while easing your anxiety and burden as much as possible. The seeDNA Genetic Medical Research Institute provides information about NIPT testing and offers support drawing on our expertise in genetic testing, so please feel free to contact us with any questions.

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Frequently Asked Questions

Q1. If my NIPT result is positive, do I have to undergo diagnostic confirmation?

A. NIPT is a screening test, and a positive result simply indicates a "high likelihood of an abnormality." Whether to undergo diagnostic confirmation is left to the wishes of you and your family. However, because it is not medically recommended to decide whether to continue or terminate a pregnancy based solely on NIPT results, undergoing diagnostic confirmation is strongly recommended so that decisions can be made based on accurate information [ref:1]. It is important to consider your future plans after receiving genetic counseling.

Q2. Should I choose chorionic villus sampling or amniocentesis?

A. Which test is appropriate depends on your gestational week, the capabilities of the testing facility, and your own wishes, among other factors. If you want results early, at 10-13 weeks of pregnancy, chorionic villus sampling is an option, but it carries a risk of placental mosaicism. From 15 weeks of pregnancy onward, amniocentesis is the more common choice, offering a relatively good balance of accuracy and safety. We recommend deciding which test is best for you in consultation with your attending physician or genetic counselor.

Q3. Should everyone undergo microarray analysis?

A. Microarray analysis is not a test uniformly recommended for all pregnant women. It is mainly performed as an additional test when structural abnormalities are found in the fetus via ultrasound, or when the cause cannot be identified through standard chromosome analysis. While it can provide more detailed genetic information, there is also a possibility of detecting a variant of uncertain significance (VOUS), so it is important to discuss thoroughly with a specialist whether to undergo this test [ref:2] [ref:3].

Q4. How much does diagnostic confirmation cost?

A. Prenatal diagnostic confirmation tests (chorionic villus sampling, amniocentesis) are, in most cases, not covered by insurance and are paid out of pocket. Costs vary by facility and testing content, but as a general guideline, chorionic villus sampling and amniocentesis typically cost around 100,000-200,000 yen. If microarray analysis is added, an additional cost of tens of thousands to over a hundred thousand yen may apply. We recommend confirming costs with the testing facility in advance.

Q5. How long does it take to get the results of diagnostic confirmation?

A. This varies by testing method and facility, but generally G-banding chromosome analysis takes about 2-3 weeks, while rapid FISH testing takes about 1-2 days (though this is a preliminary result, and the final result must be confirmed separately). Microarray analysis usually takes about 2-4 weeks, depending on the facility. The waiting period for results can be a significant source of psychological stress, so we recommend making active use of support such as genetic counseling.

Q6. What is placental mosaicism? Does it affect the baby?

A. Placental mosaicism is a phenomenon in which the chromosomal makeup differs between placental cells and the cells of the fetus itself. Because chorionic villus sampling collects and tests placental tissue, if a chromosomal abnormality confined to the placenta is detected, the fetus itself may in fact be normal. When placental mosaicism is suspected, it may be recommended to perform an additional amniocentesis to confirm the fetus's actual chromosomal makeup. The incidence is estimated to be about 1-2%.

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