Prenatal Cell free DNA (cfDNA) Screening

Prenatal Cell free DNA (cfDNA) Screening 

Alternative names- Noninvasive prenatal testing (NIPT), cell free DNA (cfDNA) testing, Non-invasive prenatal screening (NIPS), non-invasive prenatal diagnosis (NIPD), Brand names- Panorama, Harmony, Verifi, MaterniT21, InformaSeq, ChromoMap…

To the Point– Prenatal cfDNA screening is an optional blood test that can be performed at 9-10 weeks of the pregnancy and beyond that can screen for certain genetic conditions in the pregnancy and tell you if the chance of these conditions is higher or lower. Prenatal cfDNA screening also goes by the name noninvasive prenatal testing (NIPT), noninvasive prenatal screening (NIPS), cell free DNA testing, or you may familiar with some of the brand names, such as Harmony, Panorama, MaterniT21, Verifi, and InformaSeq (among others).   All of these tests are forms of prenatal cfDNA screening.  Some have referred to this test as the new gender test because in addition to screening for some genetic conditions, cfDNA screening can also predict whether the baby is a boy or a girl.  Results from NIPT are not yes or no, and positive or “high risk” results should be confirmed by a diagnostic test such as amniocentesis if more definitive information is desired.

[make_anchor_button  name=”FAQs”]  [make_anchor_button  name=”How to Decide”] [make_anchor_button  name=”Results”]

The BASICS

Prenatal cfDNA screening is an optional blood test that can be performed beginning at around 10 weeks of pregnancy and can screen for certain genetic conditions by analyzing placental DNA in mom’s blood (placental DNA usually has the same genetic make-up as that of the developing baby) to determine if there is an increased or decreased chance of certain genetic conditions.

Though this testing began as a screening for Down Syndrome, over time the list of conditions being screened has grown.  The effects of the screened conditions vary tremendously- from very mild to severe. Some of the conditions being screened are so mild that adults may not even be aware that they have the conditions (for example, individuals with 47,XXX, 47,XXY), however the effects of 47,XXX and 47,XXY vary  from person to person– learn more here.  Other conditions such as Trisomy 18 and Trisomy 13 are typically are associated with severe health and developmental concerns which usually lead to a significantly  shortened lifespan.  Prenatal cfDNA screening can also predict the gender of the baby.

Besides the common genetic conditions involving an extra or missing chromosome, many labs are now offering testing for a handful of conditions that fall under the category called microdeletion syndromes (22q11 deletion, 5p deletion, 1p36 deletion, 15q deletions).  Not all laboratories screen for the same conditions, so it is important to check with your healthcare provider to find out details regarding which conditions you are being offered screening for.

Most of the conditions screened for do not run in families.  The chance that a pregnancy is affected with a condition depends on a number of factors, including maternal age, ultrasound findings and other prenatal screening results.

If results indicate a high or increased risk, then a diagnostic test such as amniocentesis can then be performed, if the patient desires, to determine whether the baby really has the condition or not. If the results indicate a low or decreased risk, the chance the baby has the condition is small, but not zero. Keep in mind that false-positives and false-negatives do occur with cfDNA screening.  The chance of a false-positive or a false-negative result depends on the condition and also which cfDNA screening lab is used.

Because prenatal cfDNA screening only requires a blood draw on mom, we often don’t consider any risk attached to this type of testing.  However, it may be helpful to think about what these test results may mean for you. Most of the time the test will come back low risk and many women feel relief based on these results. However, if the test indicates an increased risk it may create worry and uncertainty about what to do next.  For more information, see How to Decide below.

There is a chance of not obtaining results at all (a “no-call” result).  No call results may occur due to insufficient levels of placental DNA in mom’s blood, or because of subtle variations in the DNA sequence that don’t allow the test to work properly.  Many women will get a result if they have the prenatal cfDNA screening repeated with a second blood draw.  Some studies have shown that  women who have a no-call result may have an increased chance of a chromosome condition in their pregnancyand for that reason, your healthcare provider may recommend genetic counseling or offer you the option of having diagnostic testing after receiving a no-call result rather than repeating the cfDNA screening blood work or after a repeat if it is still a no-call.

 

How It Works

DNA is contained within nearly every cell of our body.   Our cells are continuously dividing to create new cells.  As cells break down, the DNA inside the cell is released into the blood as fragments or pieces of DNA.  The “floating” DNA fragments present in the blood are known as cell free DNA (cfDNA). All pregnant women will have DNA fragments that are her DNA as well as DNA from the placenta.  The placenta develops during pregnancy and provides oxygen and nutrients to the developing baby.  The placenta usually has the same genetic information as that of the developing baby. However,  in some cases, the genetic makeup of the placenta and that of the fetus (developing baby) are not the same.  This can lead to false positive and false negative results.

There are a couple of different approaches to this testing, however, in general, the laboratory is looking for differences in the overall amount of genetic information in mom’s blood.  For example, if the testing finds an increased amount of chromosome 21 material in the blood sample, there will be an increased chance that the baby has Trisomy 21 (Down syndrome).

[make_anchors  name=”Results”]

Results

To the Point- So, bottom line with results from prenatal cfDNA screening?  They can potentially be confusing, especially when they come back abnormal, so be sure to ask your doctor or genetic counselor for clarification on any questions that you may have.  And, prenatal cfDNA results are not definitive.  Diagnostic testing such as amniocentesis is recommended to provide a more definitive answer about whether the baby does or does not have the condition. Additional things to keep in mind regarding prenatal cfDNA results include the following….

  • How well the test works for Down syndrome, Trisomy 18, Trisomy 13, and other chromosome conditions varies widely….ask your provider what results really mean.
  • Not all labs screen for the same conditions.
  • Prenatal cfDNA screening can often tell you if the baby is a boy or a girl, however, there is also a small possibility that this testing will predict gender incorrectly.
  • Prenatal cfDNA screening does not look for all chromosome abnormalities or birth defects.
  • At times, prenatal cfDNA screening can find evidence of other health conditions in mom or baby that we are not expecting (for example, the testing may reveal evidence of potential cancer in mom or another genetic condition in baby that isn’t on the list of typically screened for conditions)

As discussed above, prenatal cfDNA screening is a screening test, so results are not yes or no answers.  For most labs, you will get a separate result for each of the conditions that they are screening for.  For example, you may get a “positive/high risk “result for Down syndrome but normal results for Trisomy 13, Trisomy 18, etc. Each lab does vary in the wording of their results.  Here are some examples:

1)     Positive ( increased chance for a chromosome condition) or Negative (decreased chance for a chromosome condition)

2)     Aneuploidy detected or no aneuploidy detected (aneuploidy= extra or missing chromosome material detected), No aneuploidy detected= no extra or missing chromosome material detected)

3)     High risk/Intermediate risk/low risk

It is important to remember that extra or missing chromosome material may be detected in the mother’s blood due to reasons other than a chromosome condition in the baby such as differences between the placenta and baby’s genetic makeup or subtle variations in the DNA that causes an unusual reading of the test.

Again, if your result for one of the chromosome abnormalities returns positive/aneuploidy detected/high-risk, this does not mean the baby has the condition; it means there is an increased chance that the baby has the condition.  For more detailed information it will be very helpful to talk to your healthcare provider, such as a genetic counselor.

If the NIPT is positive/high-risk, what is the chances for someone like you, (i.e. same age, background risk) that the baby actually has the condition?”

The statistical term that answers this question for a population just like you (same age or same background risk) is called Positive Predictive Value. PPV is calculated based on knowing the sensitivity, specificity and background risk of the condition.  The lower your background risk is for a certain condition, the lower the PPV will be. 

Here’s an example- during pregnancy the chance that a 20 year old is carrying a baby with Down syndrome is about 1 in 1,000 whereas the chance for a 40 year old woman is about 1 in 100.  The chance that a prenatal cfDNA screen returning positive for a 20 year old woman is a true positive (baby actually has Down syndrome) may be about 50% with some NIPT tests, whereas for the 40 year old  woman, the chance her positive result is a true positive (baby actually has Down syndrome)  is actually closer to 90%.

Talk to your provider about what the results of your prenatal cfDNA screening really mean.

Of note, some laboratories are quoting PPVs that are very high and there is not literature to back up their claims. See this blog for more information on this topic or talk with your provider, such as a genetic counselor. 

If the prenatal cfDNA screening is normal/low-risk, what is the chances for someone like you (i.e.. same age, background risk), that the baby really does NOT have the condition?

Labs may or may not be reporting this statistic that answers this question, which is called the Negative Predictive Value (NPV).  The NPV for prenatal cfDNA screening is typically very high.  The likelihood that any of these conditions is present in a pregnancy is low and most test results will come back indicating a low-risk.  However, false negatives do occur with prenatal cfDNA screening in some cases.

Positive results on prenatal cfDNA screening- what to consider?

Since prenatal cfDNA screening is a screening test, your provider should offer you a diagnostic test, such as amniocentesis to confirm a positive prenatal cfDNA screening result if you desire definitive results. If you have chosen to do prenatal cfDNA screening for purposes of preparing for the delivery and what to expect, you do not necessarily need to have an amniocentesis; the choice is yours to make, but you should be aware that both false positive and false negatives occur with cfDNA screening. Decisions regarding whether or not to continue the pregnancy should not  be made based on cfDNA screening results alone.

Negative results on prenatal cfDNA screening- what to consider?

Many people feel reassured by their negative prenatal cfDNA screening results and do not desire any further testing. Some individuals want more thorough and definitive information regarding the chromosomes and may opt to do diagnostic testing such as, amniocentesis.  False negative results do occur with cfDNA screening, and cfDNA screening looks for a more limited number of conditions than diagnostic testing.

[make_anchors  name=”How to Decide”] 

How to Decide

Should I have prenatal cfDNA screening?

The following are some questions and thoughts to consider that may be helpful as you decide whether or not prenatal cfDNA screening is right for you…

  • How would you feel if results indicated a higher risk for a genetic condition?
    • Would you consider amniocentesis?
    • Do you think this information would help you feel more prepared?
  • If not, would you be ok waiting until the baby is born to know for sure if the condition is present if your prenatal cfDNA screening result returns high risk?
    • For example, would you consider doing anything differently if you knew the baby had a genetic condition (e.g. prepare, consider placing baby for adoption, consider not continuing the pregnancy)?
  • Does more information with the possibility of uncertainty make you anxious?
  • Some women would prefer definitive answers and since prenatal cfDNA screening cannot provide that, they may choose to go straight to a more definitive test, such as amniocentesis.
  • On the other hand, some women may feel comfortable with their chance of a genetic condition or are confident that, even if the baby did have a genetic condition, it wouldn’t alter their pregnancy plans.  Or they may prefer not to face the decision of whether or not to have an amniocentesis if the prenatal cfDNA screening comes back high risk.  In these cases some women may decide not to undergo any prenatal screening.

Ultimately, the decision to have prenatal cfDNA screening or any other prenatal screening or diagnostic test is yours to make and should reflect your own personal beliefs, values, needs and personality.

References

1) Benn P Chapman AR, Erickson K, et al. Obstetricians and gynecologists’ practice and opinions of expanded carrier testing and noninvasive prenatal testing Article first published online: 16 DEC 2013 DOI: 10.1002/pd.4272

2) Lutgendorf MA, Stoll KA, Knutzen DM, Foglia LM. Noninvasive prenatal testing: limitations and unanswered questions. Genet Med 2013 DOI:10.1038/gim.2013.126.

3) Norton ME, Rose NC, Benn P. Noninvasive prenatal testing for fetal aneuploidy clinical assessment and a plea for restraint. Obstet Gynecol 2013;121(4):847-850.

4) Pergament E et al. Single-nucleotide polymorphism-based noninvasive prenatal screening in a high-risk and low-risk cohort. Obstet Gynecol 2014;124(2 Pt1):210-8.

5)Weaver C. Tough calls on prenatal tests. The Wall Street Journal 2013:B1.
Questions? Get in touch




FAQs


What does >99% risk score on NIPT really mean?

This is a really good question.  We have actually asked numerous experts and have yet to receive a clear answer on exactly how to explain what >99% actually means.  What we do know is that in most cases, this does NOT mean that there is a >99% chance that the baby has the condition.



Why is NIPT currently recommended for high-risk pregnancies and not all pregnancies?

NIPT’s reliability has not been studied as widely in lower-risk populations.  Also it is felt that other screenings may actually perform better in lower risk women by some measures.  Currently, most of the professional societies recommend this test only be offered to women who are high-risk for one of these chromosome abnormalities.



Can I have NIPT even if I am not high-risk?

Most professional societies only recommend NIPT for patients who have an increased chance to have a baby with a chromosome condition. However, there is a chance  you may be offered this testing even if you are considered to be “low-risk”.  It may be a good idea to check with your insurance company as they may be less likely cover this testing for women who are not in a “high risk” group.  The ability of the test to answer the question, “If my test is positive/high risk, what are the chances (for someone with my same background risk), that my baby actually HAS the condition”, involves incorporating your background risk and may vary based on your age and other factors. Generally speaking, women in lower risk groups have a higher chance that a positive test result is a false positive result.



I received a “no call” result from the NIPT, what is the reason?

There are a few possible reasons that NIPT may not provide a result.  It could be due to DNA quality that is suboptimal; perhaps due to a problem with the shipping of the sample.   Some labs do not report out a result due to low fetal fraction (FF) (fetal fraction is the amount or % of placental DNA in mom’s blood).  Sometimes there are subtle, harmless variations in an individual’s DNA code that don’t allow the test to work quite right for that person.

Recent studies indicate that a no-call results may indicate an increased risk for a chromosome abnormalityand your doctor may offer a diagnostic test, such as amniocentesis based on a no-call result.

 



Is NIPT screening or diagnostic?

NIPT is considered to be a screening test and does NOT give you yes or no answers.   It has some potential benefits and drawbacks when compared to other testing options available.  Hopefully you will find the information you need to make an informed decision about the testing options here on the Genetic Support Foundation website and through continued discussions with your healthcare provider, such as a genetic counselor.

 



Are there false negatives in NIPT?

A false negative simply means that the test returned negative or low risk when in fact the baby really does have the condition.  False negatives DO occur with NIPT.  The chance of a false negative depends on a number of factors and may be higher for some conditions. If you want definitive answers about Down syndrome and other chromosome abnormalities, a diagnostic test such as amniocentesis may be a consideration for you.



How does NIPT compare to Amniocentesis and CVS?

  • NIPT is a screening test which means it can tell you if there is a higher or lower chance that a given chromosome condition is present in the baby (does not give you yes or no answers).  NIPT evaluates fragments of DNA that have come from the placenta and are present in the mother’s blood.  Usually the chromosomal makeup of the placental DNA is the same as that of the fetus.
  • Amniocentesis is considered a diagnostic test and can give you a yes or no answer with a very high degree of certainty.  Amniocentesis is an invasive test and does present some risk of miscarriage to the pregnancy (usually reported as less than 1%). However, amniocentesis evaluates cells directly from the fetus, primarily from the skin and urinary tract, and so can tell with near certainty if the baby has a given chromosome condition or not.
  • Chorionic Villus Sampling is a procedure that can be done earlier in the pregnancy that amniocentesis and involved using a needle or a catheter to biopsy small fragments of the placenta.  Usually these placental cells are the same as the genetic material in the baby and because CVS involved directly obtaining cells form the placenta, there is a larger and more definitive sample of DNA from the pregnancy to test.  Like amniocentesis CVS also is considered a diagnostic test and results are considered highly accurate.  It is important to recognize however that in some cases the fetal cells and the placental cells may have a different genetic make-up which means that there is a very small chance of false positive or false negative results with CVS.
  • The conditions that can be detected with NIPT are fewer than what can be detected with amniocentesis or CVS.  Read more about prenatal chromosomal microarray testing that can be done with amniocentesis or CVS here.  NIPT tests for a more limited set of conditions, primarily chromosome conditions such as Down syndrome, Trisomy 18 and Trisomy 13 as well as sex chromosome conditions and in some cases, some microdeletion syndromes.
  • NIPT has no risk of miscarriage associated with it; amniocentesis and CVS have a  risk of miscarriage that is less than 1%.
  • In short, NIPT is a screening test whereas amniocentesis and CVS are considered diagnostic tests.  Although sensitivity and specificity are quite high for certain conditions, NIPT CANNOT be substituted for diagnostic testing such as amniocentesis in terms of the degree of certainty associated with the results.


How does NIPT compare to other more traditional screening tests (e.g. quad screen, first trimester screen, sequential screen, integrated screen)?

  • Some studies indicate that NIPT has a higher sensitivity and specificity than more traditional screening tests for some of the conditions it screens for, especially for Down syndrome.  For example, the quad screen has a sensitivity for Down syndrome of approximately 80% versus NIPT which has a sensitivity of 90% or greater.
  • However, recent studies that include the no-call rate are calling into question whether or not the sensitivity and specificity are truly that much higher than traditional screening such as integrated screening.  http://www.medscape.com/viewarticle/839458
  • Ultimately, the thought was that the increased sesitivity and specificity of NIPT  may reduce the number of women who screen “positive” and undergo invasive testing, such as, amniocentesis..  The reason this is important is because amniocentesis and CVS are associated with a risk of miscarriage.  So, theoretically, fewer pregnancies would undergo unnecessary risk from invasive procedures.  However, given the no- call rates and as the list of conditions that NIPT screens for continues to grow, we can expect the false positve rate (and  hence, the number of amniocentesis or CVS offered/done) with this testing to rise.
  • NIPT can be done earlier in pregnancy than some of the traditional screening tests, beginning at 10 weeks gestation and NIPT can be done anytime in pregnancy after the 10 week mark
  • NIPT is looking for more chromosome abnormalities than the traditional screening tests, such as, sex chromosome abnormalities.  Also, some labs are offering add-ons for other genetic conditions in addition to the age-related chromosome abnormalities.  Ask your provider for more details on what the lab they use may be offering.  By the way, adding more conditions may not always be better.
  • Some information available on the internet regarding NIPT may lead one to believe that this test is “pretty much yes or no”, which is not the case. Although for some conditions it may have a much higher sensitivity and specificity than more traditional screening tests, NIPT does not currently equal the accuracy of amniocentesis or CVS.   If NIPT testing is abnormal, there is definitely an increased chance that the baby is indeed affected or has the chromosome abnormality, but results need to be interpreted with caution.  Current guidelines recommend that any abnormal NIPT be followed up with a diagnostic test, such as CVS or amniocentesis, to confirm these findings.  There have been MANY cases where NIPT came back positve/high-risk and the baby did NOT have the condition.  Likewise, there have been several cases of negative/low-risk NIPT result and the baby did have one of the conditions that NIPT screens for.
  • Currently, NIPT is NOT regulated by the FDA. Most of the information that we have regarding how “good” these tests are comes from studies funded by the labs and/or authored by individuals associated with one of the labs2.
  • NIPT looks for some of the same genetic conditions as traditional screening tests, however, not all.  Most of the more traditional screening tests look for evidence of open neural tube defects, like spina bifida, and NIPT does not.  However, this can be screened for by ultrasound and a separate blood draw in the second trimester.  First and second trimester ultrasounds and other traditional screening tests also have the potential to detect other birth defects and potential pregnancy complications that may be missed by NIPT.


Where can I find additional information and resources regarding NIPT?


Info





Genetic Support Foundation
Copyright © 2015 Genetic Support Foundation, Inc