Pregnancy is an exciting time, but it often comes with a lot of questions. Many future parents seek as much information as they can to make proactive decisions during pregnancy care, and genetic insights play a big role here.
One increasingly used option is cell-free fetal DNA analysis (cffDNA), a simple blood test that can provide early information about the health of the developing baby.
We’ll explain cell-free DNA analysis, when it’s typically done, and what it can (and can’t) tell you. Whether you’re only exploring your options or already planning your prenatal screenings, this guide can help you make informed choices.
What is a cell-free fetal DNA analysis?
Cell-free fetal DNA analysis is a noninvasive prenatal screening test that uses only a blood sample from the mother to look for specific chromosomal conditions in a baby during early pregnancy.
During pregnancy, small fragments of your baby’s DNA — called cell-free fetal DNA (cffDNA) — circulate in your bloodstream. These fragments mostly come from the placenta and reflect your baby’s genetic makeup.
Starting around the 10th week of pregnancy, there’s usually enough fetal cffDNA in your blood for a lab analysis. The lab looks closely at this DNA to check for extra or missing copies of specific chromosomes.
Humans typically have 46 chromosomes, arranged in 23 pairs:
22 pairs of autosomes (also called trait chromosomes), which determine most of your body’s characteristics
1 pair of sex chromosomes, which determine chromosomal sex (XX or XY)
Each parent contributes one chromosome to each pair. If there's an extra copy in one of those pairs (called a trisomy), it can affect how the baby’s body and brain develop. The cffDNA test can also detect if there is a missing chromosome, typically one X chromosome in females (called monosomy X).
Source: Artem Podrez
Because cffDNA analysis only involves a blood draw from the mother, there’s no physical risk to the baby.
Bonus read: The terms cell-free DNA test and NIPT are often used interchangeably, but they’re not the same. Learn about the difference here.
What does a cell-free fetal DNA analysis test for?
Cell-free fetal DNA analysis typically assesses the likelihood of chromosomal conditions in a developing baby, but it can also offer additional insights.
Here is what it usually reveals:
Down syndrome (trisomy 21): Caused by an extra copy of chromosome 21, this is the most common chromosomal abnormality. It can affect learning and development, but many people with Down syndrome live long, meaningful lives.
Edwards syndrome (trisomy 18): A serious condition caused by an extra chromosome 18; it often leads to severe developmental issues, and many affected pregnancies do not result in a live birth, or the baby may not survive beyond the first year.
Patau syndrome (trisomy 13): This rare and severe condition, caused by an extra chromosome 13, also significantly affects development and survival.
Sex chromosome abnormalities: These involve changes in the X or Y chromosomes. The test may be able to detect Turner syndrome, where a baby girl has only one X chromosome, which can lead to short stature, heart problems, and infertility. It may also detect Klinefelter syndrome, where a baby boy has an extra X chromosome (XXY), which may affect physical development, learning, and fertility.
Rh blood type compatibility: If you’re Rh-negative and your baby is Rh-positive, this mismatch can sometimes cause health problems during pregnancy. Knowing about it early allows your care team to take preventive steps for your baby and you.
Source: Pavel Danilyuk
In some cases, cffDNA testing can also help determine the baby's sex, which is useful when ultrasound results are unclear. Studies show up to 99% accuracy, especially if the test is done after week 12, but accuracy drops significantly if done before week 7.
When is cell-free fetal DNA analysis done, and what’s next?
Cell-free fetal DNA testing can be done as early as week 10 of pregnancy, and the results are usually ready within 10–14 days.
The results fall into one of three categories:
Low risk (negative result): No major chromosomal differences were detected, so it’s very unlikely that your baby has the condition tested for.
High risk (positive result): A higher chance of a specific chromosomal condition was detected.
Inconclusive or no-call: Sometimes, the test doesn't provide a clear result, most commonly because of low fetal DNA levels in the blood sample. Your provider may recommend repeating the test or exploring other options.
It’s important to know that this test is a screening, not a diagnosis. It can tell you if there’s a higher or lower chance of a condition, but it can’t confirm whether your baby actually has it.
If your results are high risk, further diagnostic testing is recommended. The likelihood that a positive result reflects a true condition depends on your individual risk.
In high-risk groups, about 83 out of 100 people with a positive result for Down syndrome are truly affected. In lower-risk groups, that number may be closer to 33 out of 100.
Who is the cell-free fetal DNA analysis test for?
Anyone who is at least 10 weeks pregnant can do cell-free fetal DNA screening, but it’s most commonly recommended for those at a higher risk of having a baby with a chromosomal condition.
The mother may be considered high risk if:
She’ll be 35 or older at the time of delivery
She has had a previous pregnancy or baby with a chromosomal condition
Her ultrasound or standard prenatal tests showed something unusual
She has had an organ transplant
She is overweight
Source: Gustavo Fring
Your healthcare provider may recommend meeting with a genetic counselor to help you compare screening options, even if you’re at lower risk.
Note that cffDNA screening isn’t used in pregnancies with three or more babies.
Bonus read: Learn about other noninvasive prenatal tests:
How reliable is fetal DNA analysis through maternal blood?
Cell-free DNA screening is highly accurate, but remember that it screens primarily for the most common trisomies, not all possible chromosomal conditions, and it only shows increased risks.
Studies show that cffDNA screening is highly accurate in detecting true positives and negatives, outperforming traditional screening methods like the sequential screen or the quadruple marker test.
The table below shows cffDNA test detection rates for the most common chromosomal abnormalities:
Condition | Detection rate |
Down syndrome (trisomy 21) | 99% |
Edwards syndrome (trisomy 18) | 97% |
Patau syndrome (trisomy 13) | 87% |
Some factors that can affect accuracy include:
Twin pregnancies
Presence of a nonviable second fetus
Testing done early in the first trimester
Fetal fraction and maternal DNA ratio
Placental mosaicism
Technical reasons, such as low fetal DNA levels
It is also possible for the cffDNA test to give a false-positive result, which happens in about 5% of cases.
Many parents who have done this test believe that it was an excellent decision:
However, for some, this test only brought feelings of uncertainty:
What is the advantage of cell-free DNA analysis?
Cell-free fetal DNA analysis is a major advancement in prenatal genetic testing because it helps avoid unnecessary invasive procedures. Some of the key advantages are:
Noninvasiveness: Unlike amniocentesis or chorionic villus sampling, which carry a miscarriage risk of about 0.5–1%, cffDNA testing requires only a blood draw, making it much safer and more accessible for mothers who cannot undergo invasive tests.
Early testing: It can be performed earlier than traditional serum screenings or invasive tests, so you can get important information sooner.
High accuracy for common trisomies: cffDNA analysis reliably detects common trisomies, with very low false-positive rates.
Additional information: The test also identifies fetal sex, sex chromosome abnormalities, fetal Rh factor status for RhD-negative mothers, and some microdeletion syndromes, though with lower sensitivity.
Emotional and decision-making support: The noninvasive nature and accuracy reduce anxiety, giving you more time and confidence to consider next steps.
Healthcare benefits: Since its introduction, cffDNA testing has led to a significant reduction in invasive diagnostic procedures (76% decrease in amniocentesis and 54% decrease in chorionic villus sampling), lowering risks and costs.
Source: Mart Production
What are the limitations of cell-free fetal DNA analysis?
While cell-free fetal DNA testing offers many benefits, it also has important limitations you should keep in mind:
Limited scope: It screens only for a select group of conditions, not all possible birth defects or complications.
Results don’t reflect individual risk: Test reports often present results as only “positive” or “negative” without factoring in your personal background risk, which can lead to misunderstandings about the true chance of an affected pregnancy.
May reveal unexpected findings: Sometimes, cell-free fetal DNA testing can pick up genetic changes in the mother’s DNA that aren’t related to the baby’s health. This can cause worry or confusion and often requires additional tests and consultations to understand what these findings mean, all of which can be stressful for expecting parents.
Need for thorough counseling: Because the test is easy to perform and results seem straightforward, some women may undergo it without fully understanding its limitations, leading to false reassurance or confusion.
Bonus read: Learn about additional genetic testing options:
Options beyond fetal cffDNA testing
Cell-free fetal DNA analysis offers valuable early insights, but some families seek a deeper understanding of their health and genetic status — whether due to a known inherited condition, inconclusive screening results, or a desire for greater peace of mind.
In such cases, expanded genetic testing, such as carrier screening, is an option worth considering.
Carrier screening helps identify whether one or both parents carry genes for inherited conditions that could be passed on to their children, and that cffDNA testing does not detect. These tests are done before pregnancy, giving future parents time to understand their options and make informed decisions well in advance.
For people using IVF, carrier screening is especially valuable. If both parents are carriers of the same condition, there’s a higher chance the condition could be inherited. In these cases, embryo genetic testing (usually preimplantation genetic tests, such as PGT-A, PGT-M, and PGT-P) can identify which embryos have the lowest health risk and are suitable for transfer.
How Nucleus supports your prenatal journey
With whole-genome carrier screening, the Nucleus Family DNA test kit can uncover [NUM_CONDITIONS_SCREENED]+ potential inherited conditions, helping you understand what genetic traits you and your partner might pass on to your child. It can screen you for cardiovascular, neurological, metabolic, and mental health conditions, among other aspects.
What makes the test stand out is that it can also detect rare and chronic genetic carriers that other commercial tests may miss. Nucleus testing is clinical-grade and physician-ordered, so you can use your results to discuss specific health risks with your doctor.
Genetic testing can get expensive, especially if you have to do multiple separate tests. Nucleus’s comprehensive approach offers more coverage in one test, which can reduce the need for additional screenings down the line. Plus, it’s eligible for HSA/FSA.
If you’re in the pre-pregnancy stage and considering IVF, Nucleus Embryo is another tool that may help you. It's a genetic optimization software that uses embryo testing data (from PGT-P testing) to assess adult-onset and chronic health risks, such as:
Diabetes
Heart disease
Neurological conditions
Certain types of cancer
You can compare up to 20 embryos in an interactive dashboard, so you and your IVF specialist can decide which one is the best for transfer.
How to get started with Nucleus
If you want to get screened for carriers before or during pregnancy, here’s what to do:
Provide your personal information
Order the test kit
Once you send your sample, you’ll receive your results in up to eight business days.
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Featured image source: Mart Production
