Empowered Pregnancy Choices - Non-Invasive Prenatal Screening - The NIPT Test

By: Aunt Doula (12/06/2022)

Around the globe, non-invasive prenatal screening tests – NIPT’s or NIPS – have become an unregulated standard of for-profit screening tests to offer pregnant people, typically in their first trimester. Sold with claims as high as 99% accuracy and suggesting a significant ‘peace of mind’ spin, NIPS have become a lucrative market acting with the promise of screening for potential issues without risks to the pregnancy. However, when these tests are offered and performed in low-risk pregnancies it opens up a significant population to unnecessary invasive procedures, increased worry, and financial burdens that has very little return. In the US, the FDA has not approved any NIPT test and labs are allowed to claim just about anything, confirmed internally by their own studies, and charge what they see fit. There is no standardization of methodology or mechanisms by which a ruling body can confirm the claims of these companies. While they have “good enough” results that a significant portion of people around the world submit for testing, understanding the scope of the test, its limitations, and its usefulness to your situation is extremely important to learn about before you move forward with testing. Anyone who wishes to have an NIPT test should do so ideally with the guidance of a genetic counselor prior to the testing, and positive or abnormal results delivered with significant care, education, support and clear next steps provided.

Under the umbrella of Non-invasive pre-natal screenings – NIPS – is the specific test referred to as that NIPT. Any test that is listed as an NIPT should include screening at a minimum for the increased risk of Trisomy 13 (Patau Syndrome), Trisomy 18 (Edwards Syndrome), Trisomy 21 (Down Syndrome), and aneuploidy (number of chromosomes other than the normal two) of the sex chromosomes X and Y which include Trisomy X (Turner Syndrome), Monosomy X, and XXY (Klinefelter syndrome). As companies have been expanding into this growing market, some offer screening for aneuploidy of additional chromosomes, microdeletions and carrier conditions like Cystic Fibrosis and Spinal Muscle Atrophy.

Also under the umbrella of NIPS are tests known as “First Trimester Screening” which includes an ultrasound to look at the fetus’s Nuchal Translucency measurement along with a blood test for two hormones, HCG and PAPP-A, and then another set known by multiple names done in the second trimester. Second Trimester Screening aka “Maternal Serum Screening”, “Triple Screen” and “Quad Screen” are all blood tests that look at hormone levels produced by the placenta to determine increased risk of chromosomal Trisomy’s 21 & 18, as well as increased risk of neural tube defects.

This post will be covering the basics of the NIPT test, the first and second trimester screening tests will be covered in another post and linked here when completed. We will cover the most pressing question first – What does a ‘positive’ result actually mean? Then we will cover when the test can be performed, who receives NIPT testing, choosing if you should pursue NIPT testing, what the NIPT testing is, how NIPT testing determines risk, and why other tests may be used instead of or in addition to it. We will also cover certain situations in which the NIPT test fails to return an assessment and other rare result outcomes and their meaning.

Before getting to these questions, it is important to note the terms “Fetal Fraction” and “PPV%” as they are usually the first thing people see and don’t understand.

“Fetal Fraction” is the amount of placental debris that was retrieved and separated from the maternal blood sample. Most tests require a minimum percentage in order to have accurate results. This varies between companies; the ideal amount is considered between 10-14% and the minimums tend to be anywhere from 2%-4% depending on the lab. If your test returns as “insufficient fetal fraction”, it simply means there was not enough placental debris recovered from the blood sample to perform the testing.

“PPV%” is the Positive Predictive Value Percentage – This is a very misunderstood and confusing result on the NIPT. This percentage is the likelihood that the test is correct, it is NOT the percent chance your baby has the condition. For example – if you had a ‘positive result of increased risk for Trisomy 18 with a PPV% of 78.5%’, this means that there is a 78.5% chance that the test is correct that there is an increased risk of Trisomy 18. That is the only meaning it carries. It directly relates to the accuracy of the test being correct there is increased risk for Trisomy 18, it does not have anything to do with the direct chances of the fetus having Trisomy 18.

What a "positive" result actually means for your pregnancy

*The single most important thing to know and understand about any NIPT or Maternal Blood Testing/Screening is that it is only a measure of risk.* It cannot and does not diagnose any condition of the fetus, and it's entire purpose is to screen for pregnancies that require invasive testing to rule out genetic disorders. If you have received a "positive" NIPT test result the only thing that definitively means is that more testing is necessary to know if there truly is a genetic anomaly.

A "Positive" result on an NIPT indicates "Increased Risk" and only Increased Risk that the fetus may have a genetic condition. A ‘positive’ test result or increased risk value only informs that more invasive testing would be necessary to determine a true genetic anomaly in the fetus. Without further testing, even in the presence of soft markers on ultrasound that correlate to the screened positive risk anomaly, no irreversible decisions should be made on the NIPT and ultrasound markers results alone.

When is an NIPT test performed?

Depending on the lab, NIPT testing can be done as early as 9 weeks gestation, however it is typically drawn around 12 weeks to ensure a sufficient amount of placental debris is available for testing. By performing the blood draw for the NIPT at 12 weeks, the Nuchal Translucency ultrasound can be performed (if indicated) at the same visit. The NIPT can technically be drawn at any point of the pregnancy after 9 weeks, however it has a diminishing use if a severe issue is already suspected, and invasive testing may be preferred to get answers in a timely manner.

Who receives an NIPT test?

NIPT testing is offered to most people receiving modernized obstetric care. While it’s use was intended to be for high-risk pregnancy screening for conditions such as advanced maternal age, its use has expanded into low-risk pregnancies as a “reassurance” screening that most people opt-in to not realizing that they may get more than they bargained for in a false positive. For this reason, many national and private health plans are beginning to not cover NIPT tests unless there is a high-risk qualification indicating a need for screening that could lead to invasive testing. In the absence of genetic family history, advanced maternal age, prior pregnancy losses or other high-risk situations as determined by your provider, pursuing the NIPT test may not be worth your money, or the stress a false positive can bring. Choosing to have an NIPT test or any maternal screening is a discussion you should have with your provider in depth to determine if it is worth it for all considerations.

What is the NIPT test?

The NIPT test is a 'maternal blood screening' meaning that the pregnant person will have their blood drawn into a vial like any other blood test you have probably had. This blood is then separated into its many parts, and one of those parts is placental debris. After about 10 weeks' gestation as the pregnancy progresses the pregnant person's blood is filtering into and through the placenta. When it travels through, microscopic pieces (debris) of the placenta ends up being picked up into the pregnant person's blood. In that debris is placental genetic material that is (usually) the same as the baby. This placental debris is separated from the rest of the maternal cells and tested independently. *Cases where the genetics of the placenta and the genetics of the baby don't match will be covered later on in special circumstances*

The now-separated placental debris is tested for presence of particular amounts of at least the 5 specific chromosomes - 13, 18, 21, X, Y. The amount of cells that are collected and separated out from the maternal DNA is called the "Fetal Fraction" and depending on the lab if there are not enough cells for testing they may be unable to complete the test with the sample given. The lab will give guidance on if another specimen would be beneficial or if invasive testing should be pursued instead.

The basic/standard NIPT only tests for abnormalities within these 5 chromosomes - 13,18, 21, X & Y. If you do not want the gender of your baby reveled, you will need to tell your doctor to have the lab keep those results separate. As NIPT (Umbrella) testing has grown and offerings widened, some companies have started to offer screening for additional chromosomal aneuploidy or for other common abnormalities. It is important when you choose to have any maternal screening test, you understand which test you are having, with what lab company, what chromosomes they screen, and if your insurance covers it. It is also extremely important to know how often the test results are correct in detecting the problem it is flagging "positive" or "high risk." This is known as PPV% which we will cover separately below.

The NIPT test is a screening tool that only looks at the placental debris that is separated out of the maternal bloodstream. It is not genetic material from the fetus - the genetic cells that became the fetus separated away from the cells that become the placenta early in the development and founding days of the pregnancy. While the material for both came from the same embryo, in the cell division and determination process they became distinct groups of cells designated for different purposes - this means that cells that broke away and formed the placenta may not be present identically as in the baby, and vice-versa. As such, you must understand the limitations of the NIPT screening and what is actually being tested - the placental DNA debris.

The testing and examples for how results are determined

In general, testing takes an average of 2 weeks to get results returned. In some places it can be significantly longer depending on how many labs are available to perform testing or if testing must be done under the supervision of a local government.

The test itself is a measurement of the debris that determines how much genetic material should be detected given a baseline from the labs internal control. This may vary by company and is often proprietary however the goal is the same - discover if there is an excess or lack of material expected. *The following would be an example using a chosen number of 100∆ for a baseline material normal result for explanation and does not represent any specific lab results. *

If the control amount expected of chromosome material is say 100∆ (representing the normal balanced amount) the specimen to be tested is put into its machine and it looks at the cells and compares the amounts of detected materials of chromosomes 13, 18, 21, X and Y.

• A low-risk report for a boy that would return "negative" would in this scenario be the expected results for chromosomes 13, 18, 21, X & Y to be 100∆ each. All chromosomes tested had the appropriate representation levels of 100∆ indicating low risk/negative results.

• A low-risk result for a girl,that would return "negative" would have been 100∆ for chromosome 13, 18, & 21. For the X chromosome the result would be 200∆ (Two X chromosomes, each at 100∆ for a girl means 200∆ expected) and a result of 0∆ (zero) for the Y chromosome.

• When there is a problem, in this example framework say for a boy with elevated down syndrome risk, there is an elevated amount of the 21st chromosome detected. So in our example the test results come back 100∆ for chromosomes 13, 18, X & Y, and 150∆ for chromosome 21. Extra material than expected of the 21st chromosome was detected, therefore the test flags positive for high-risk possible down syndrome and further testing is required to confirm that this result is indicative of the genetics in the baby.

• Another example in this framework of a girl with increased risk of Monosomy X, the test would have returned 100∆ for chromosomes 13, 18, & 21. It would return 0∆ for Y and 100∆ for X (half the amount of material expected - for a 'normal' girl, XX, would be 200∆) Less material than expected was detected for the X chromosome, and with no Y chromosome material, the increased risk is that there is only one X worth of chromosome material being detected, indicating a possible risk of Monosomy X.

• An example of an indeterminate sex result is possible and using the same numbers as above, a sex chromosome anomaly could present with chromosomes 13, 18, & 21 low risk returning at 100∆. However an increased representation of the Y chromosome compared to the X chromosome. Say 200∆ Y chromosome and 100∆ X chromosome. This result could indicate a baby with an extra Y chromosome, known as 47, XYY.

These numbers are only applicable to this example and numbers picked were for ease of understanding. This is not an exhaustive list of possible returns of results. No NIPT testing provides these kinds of direct numerical values for chromosome material, this was for educational understanding only

Other Tests Your Doctor may Consider

There are a number of ‘maternal serum screening’ tests available as of the writing of this article. With the stand-alone NIPT screening being contested as a first line of screening for every pregnancy, you may be offered First Trimester Screening if you qualify. First Trimester Screening – FTS – is a 2-part test done between the 11th and 13th week of gestation and includes having a blood test for HCG and PAPP-A hormone levels, and a nuchal translucency ultrasound. You can learn more about the FTS however one does not necessarily replace the other, and having both can be complimentary. If you are offered one covered under your insurance, if something came back abnormal that may authorize the coverage of the other. Again, this is an important discussion to have with your provider or a genetic counselor before pursing testing so you know what to expect, what the results indicate, and what comes next if you have a positive/increased risk results.

In the second trimester, serum screening options include the “Triple Screen” (outdated and less accurate) test OR the “Quad Screen” test. These serum screens look for increased risk of issues in the fetus based upon hormone levels detected withing the mothers blood coming from the placenta. Please see the post on those tests .

Typically, if you had screening tests performed in the first trimester, it is unlikely you would need second trimester screening as well, however there may be circumstances that dictate the need for this additional blood draw.

Odd Results, Rare Findings, & False Negatives

• The NIPT test is limited in what it can do, and while the range is increasing, the accuracy of those results must always be taken into account with the PPV%. Odd results may be reported for chromosomes outside 13, 18, 21, X & Y through Whole Genome Sequencing methods or if there was sufficient material to warrant the notation by the lab. If there is a section in your results that is listed as or similar to “Rare Other Aneuploidies” this means the lab did screen outside the base 13, 18, 21, X & Y chromosomes but you must discuss with a genetic counselor how accurate the results are and take the results for what they all are – a screening. Remember that the screening results and predictive percentages cannot tell you anything except that further testing would be required to test the actual genetic code of the fetus to know for sure if a genetic condition is present. These results may also come with a notation of an “Unknown source” meaning that the lab can’t ascertain with certainty that the genetic material they discovered came from the fetus, a vanishing twin, multiple fetuses or maternal contamination. It may note the possibility of “Maternal Origin” meaning that the genetic condition flagged for increased risk may be present in the pregnant persons DNA and contaminating the results of the fetus’s risk assessment. This is not a comprehensive list of odd findings but know that if you have received a strange notation or were not provided with a result, you are not alone.

• Rare Findings on an NIPT result include a positive/high-risk result for multiple or all chromosomes. One reason for this result is a very rare condition called “Triploidy” where the fetus has 69 chromosomes, 3 of every chromosome instead of 2, which can occur when two sperm fertilize one egg at the same time. While this is exceptionally rare, it has happened and is sadly a fatal condition in all cases.

The other reason for this is cancer in the pregnant person that causes a return of positive/high-risk on the NIPT due to the extra genetic material of the cancer cells in the blood sample being tested. This is also exceptionally rare.

• False Negatives are possible while rare and can happen when the fetus contains a genetic condition the NIPT screens for, however the placenta does not share the same genes as the fetus. The reasons for this are complex and beyond the scope of this post, however worth mentioning as it is a possible outcome.

The opposite and much more common outcome of a False Positive occurs when the placenta contains a genetic condition that the fetus does not, known as Confined Placental Mosaicism.

The recommendations of multiple organizations in regard to NIPT testing is that it should be reserved for high-risk pregnancies and include pre and post testing counseling to support parents through the possible outcomes. While this may happen for some, it is certainly not the case for the majority of parents. Those who end up in limbo with nowhere to turn will hopefully find their way here to help bridge the gap. If you need someone to talk to and don’t want to make a post, please don’t hesitate to contact me directly.