Cell-Free DNA Fetal Fraction Calculator
Cell-Free DNA Fetal Fraction Calculator
The placental share of the cell-free DNA in a maternal plasma sample — the quality metric that decides whether a prenatal screening result can be issued at all, and why a no-call is not a negative result.
Cell-Free DNA Fetal Fraction
Fetal, total cfDNA → %276 genome equivalents per millilitre of placental cell-free DNA in a total of 2,400
Formula
reporting floor: laboratory-set, commonly 4%, published floors range from about 2 to 4%
- fetal cell-free DNA
- placental in origin, not fetal in the literal sense. It comes from apoptosis of trophoblast, which is why a confined placental mosaicism produces a screening result that does not match the fetus, and why the DNA clears within hours of delivery rather than persisting between pregnancies
- total cell-free DNA
- maternal and placental together. The great majority is maternal, from turnover of the mother’s own blood cells, which is the mechanism behind the body mass index effect: more maternal cell-free DNA in circulation dilutes the same placental contribution to a smaller fraction
- the reporting floor
- not a standard but a laboratory decision, commonly 4% and published anywhere from about 2 to 4%. Below it the shift in chromosome counts produced by a trisomy is too small to separate from counting noise, however deeply the sample is sequenced
- what it is not
- THE POINT OF THE PAGE: fetal fraction is not the z-score and not the risk score. It is a property of the sample. The aneuploidy result is computed separately, from the proportion of sequence reads assigned to each chromosome, and it is only interpretable because the fetal fraction is known — the two are linked but they are not the same number
- why a no-call is not negative
- because nothing has been screened. A failed test leaves the prior risk untouched, and the failure is not independent of the answer: trisomy 18 and trisomy 13 run with lower fetal fractions than euploid pregnancies, so the test fails preferentially on some of what it was ordered to detect
Worked example
276 genome equivalents per millilitre of placental cell-free DNA in a total of 2,400
Fetal fraction = 276 ÷ 2,400 × 100 = 11.5%, close to the 11.6% median of a series of more than 150,000 screened pregnancies
The other 2,124 genome equivalents — 88.5% of the sample — are maternal, and that is the normal state of affairs
Now hold the placental contribution and raise the maternal one, which is what a higher body mass index does. The same 276 in a total of 3,400 is 8.1%; in 6,000 it is 4.6%, and the sample is close to the reporting floor without anything having changed about the pregnancy
That gradient is observable: median fetal fraction fell from 13.3% below a body mass index of 18.5 to 8.8% at 30 or above, in the same large series
Gestational age moves it the other way, but slowly in the window where screening is usually done — about 0.44 percentage points per week from 10 to 12.5 weeks, and only 0.083 per week from 12.5 to 20 weeks, before rising steadily after about twenty weeks
None of this is the aneuploidy result. That comes from the chromosome read counts, and this figure is the quality metric that decides whether it can be computed at all
What moves the fetal fraction
| Factor | Direction and size | Source of the figure |
|---|---|---|
| Maternal body mass index | Median fetal fraction 13.3% below 18.5 kg/m², 11.9% at 18.5–25, 10.2% at 25–30 and 8.8% at 30 or above | A series of 153,306 screened pregnancies |
| Maternal weight, extreme | No-call rate for low fetal fraction at 9–12 weeks: 0.14% below 150 lb against 17.39% above 400 lb | A cohort study of timing and redraw in obesity |
| Gestational age | +0.44 percentage points per week from 10 to 12.5 weeks, +0.083 per week from 12.5 to 20, then rising steadily after about 20 weeks | A review of factors affecting fetal fraction |
| Trisomy 21 | Higher than euploid — median 12.5% against 11.6%, a ratio of about 1.2 | The same 153,306-pregnancy series, and an independent cohort |
| Trisomy 18 | Lower than euploid — median 9.3% against 11.6% | The same series |
| Trisomy 13 | Lower than euploid — median 10.9% against 11.6% | The same series |
| Triploidy | Associated with low fetal fraction; no percentage is quoted here because none could be verified | A fetal-fraction-based risk algorithm exists specifically for trisomy 13, trisomy 18 and triploidy in women with low fetal fraction |
| Twin pregnancy | Higher in total — about 1.6 times a singleton — but the figure that matters is the smaller placenta’s share, which is not the total | A cohort study of maternal and fetal characteristics |
What a no-call means, and how much is disputed
| Question | What the evidence says |
|---|---|
| Is a failed test associated with aneuploidy? | Guidance is unambiguous that it is: women with failed cell-free DNA tests are at increased risk for aneuploidy and need careful counselling about further testing, including the offer of diagnostic testing |
| By how much? | Disputed. Published estimates of aneuploidy risk in low-fetal-fraction cases span 2.7% to 23.3% |
| Does every low-fetal-fraction failure carry that risk? | No. In one large single-laboratory series, successfully redrawn low-fetal-fraction samples were positive in 1.5% against 1.1% in the overall population, a difference that was not significant, with no enrichment of trisomy 13 or 18. The authors concluded that caution is needed in generalising aneuploidy risk to all such failures |
| Does maternal weight explain it? | Partly. Low-fetal-fraction cases in that series averaged 215 lb against a population average of 166 lb, and the authors argue that patient factors should be taken into account rather than aneuploidy risk being assumed |
| What does not change with the dispute | That nothing has been screened. Whatever the residual risk, a no-call leaves the prior risk in place and must not be recorded as a low-risk result |
A quality metric that is not independent of the answer
Cell-free DNA in maternal plasma is overwhelmingly maternal. It comes from the turnover of the mother’s own blood cells, and into that background the placenta contributes a minority share: the fetal fraction, conventionally about a tenth of the total in the first trimester, with a median of 11.6% in a series of more than 150,000 screened pregnancies. The word fetal is a convenient inaccuracy — the DNA is placental, shed by apoptotic trophoblast, which is why confined placental mosaicism produces screening results that do not describe the fetus, and why the DNA clears within hours of delivery instead of carrying over into the next pregnancy.
The fraction matters because it sets how big a signal an aneuploidy can produce. Screening works by counting sequence reads assigned to each chromosome and looking for a small excess: a trisomic placenta contributes one and a half copies of that chromosome where it should contribute one, and the excess in the whole sample is that difference diluted by the maternal share. Halve the fetal fraction and you halve the shift being looked for, while the counting noise stays where it is. That is why a floor exists at all, and why no amount of extra sequencing rescues a sample below it. The floor is a laboratory decision rather than a standard: 4% is the commonest published figure, one large series states it explicitly as its lowest limit, a review describes laboratories setting it anywhere from 2 to 4%, and at least one laboratory operates at 2.5%.
What drives the fraction down is worth separating into the numerator and the denominator. Maternal body mass index acts on the denominator — more maternal cell-free DNA in circulation, the same placental contribution, a smaller fraction — and the gradient is clear in every large cohort: 13.3% below a body mass index of 18.5, falling to 8.8% at 30 or above, and at the extreme a no-call rate of 17.39% at 9 to 12 weeks in women weighing over 400 lb against 0.14% below 150 lb. It is worth noting that the only meta-analysis of the question, pooling studies that compared low-fraction with normal-fraction groups, did not find the body mass index difference statistically significant, while it did find one for gestational age. The cohorts and the pooled analysis disagree, and the honest summary is that body mass index is the largest influence visible in every large single series and the pooled evidence is weaker than that makes it sound. Gestational age acts slowly in the window where screening is done — about 0.44 percentage points per week between 10 and 12.5 weeks and only 0.083 per week thereafter — which is why a redraw a fortnight later helps less than intuition suggests, though it still helps.
The aneuploidies act on the numerator, and this is the part that makes a no-call dangerous to file away. Trisomy 21 runs with a slightly higher fetal fraction than euploid pregnancies; trisomy 18 and trisomy 13 run lower — median 9.3% and 10.9% against 11.6% in the same large series — and triploidy is associated with low fractions too, to the point that a risk algorithm exists specifically for those three conditions in women whose fetal fraction is too low to report. So the test fails preferentially on part of what it was ordered to detect. Guidance follows from that: women with failed tests are at increased risk for aneuploidy and need careful counselling about further testing, including the offer of diagnostic testing. How much increased is genuinely contested — published estimates run from 2.7% to 23.3%, while one large single-laboratory series found successfully redrawn low-fraction samples positive in 1.5% against 1.1% in the overall population, a difference that was not significant. The dispute is about magnitude. It is not about the instruction, which survives either reading: a no-call means the pregnancy has not been screened, the prior risk is unchanged, and the result must never be recorded as low risk. And one final distinction that gets blurred on reports — the fetal fraction is a property of the sample, not of the fetus. The z-score and the risk score are computed separately from the chromosome counts. A high fetal fraction does not make a result normal, and a marginal one does not make it abnormal.
Frequently asked questions
How is fetal fraction calculated?
Fetal fraction is the placentally derived cell-free DNA as a percentage of the total cell-free DNA in the maternal plasma sample: fetal ÷ total × 100. Both figures must be in the same units, since it is a ratio. A typical first-trimester value is around 10 to 12%, with a median of 11.6% in a series of more than 150,000 screened pregnancies.
What is the minimum fetal fraction for a reportable result?
There is no universal standard. Four per cent is the commonest published floor and is used explicitly by large series; a review describes laboratories setting it anywhere from 2 to 4%, and at least one laboratory reports down to 2.5%. Below the floor, the shift in chromosome counts a trisomy produces cannot be separated from counting noise however deeply the sample is sequenced.
Why does maternal BMI lower the fetal fraction?
Because it raises the denominator rather than lowering the numerator. More maternal cell-free DNA in circulation dilutes the same placental contribution. Median fetal fraction fell from 13.3% below a body mass index of 18.5 to 8.8% at 30 or above in one large series, and at extreme weight the no-call rate at 9 to 12 weeks reached 17.39%.
Does a no-call mean the result is normal?
No. A no-call means nothing has been screened and the prior risk is unchanged. Guidance states that women with failed cell-free DNA tests are at increased risk for aneuploidy and need counselling about further testing including diagnostic testing. The size of that increase is disputed — estimates range from 2.7% to 23.3%, and one large series found no significant enrichment — but the instruction is the same either way.
Do some aneuploidies themselves lower the fetal fraction?
Yes, and in the unhelpful direction. Trisomy 18 and trisomy 13 run with lower fetal fractions than euploid pregnancies — medians of 9.3% and 10.9% against 11.6% — and triploidy is associated with low fractions as well. Trisomy 21 runs slightly higher. So the test fails preferentially on part of what it was ordered to find.
Is fetal fraction the same as the risk score?
No. Fetal fraction is a quality metric describing the sample: how much of the cell-free DNA came from the placenta. The aneuploidy result is a separate calculation from the proportion of sequence reads assigned to each chromosome, interpretable only because the fetal fraction is known. A good fetal fraction does not make a result normal.
Related calculators
References
- Deng C, Liu J, Liu S, et al. Maternal and fetal factors influencing fetal fraction: a retrospective analysis of 153,306 pregnant women undergoing noninvasive prenatal screening. Front Pediatr. 2023;11:1066178.
- Deng C, Liu S, et al. Factors affecting the fetal fraction in noninvasive prenatal screening: a review. Front Pediatr. 2022;10:812781.
- Mousavi S, Shokri Z, Bastani P, et al. Factors affecting low fetal fraction in fetal screening with cell-free DNA in pregnant women: a systematic review and meta-analysis. BMC Pregnancy Childbirth. 2022;22:918.
- Society for Maternal-Fetal Medicine. SMFM Statement: clarification of recommendations regarding cell-free DNA aneuploidy screening — on the management of failed tests.
- Hopkins MK, Koelper N, Caldwell S, et al. Obesity and no call results: optimal timing of cell-free DNA testing and redraw. Am J Obstet Gynecol. 2021;225(4):417.e1–417.e10.
- Caldwell S, Sagaser K, Nelson Z, et al. Not all low fetal fraction cell-free DNA screening failures are at increased risk for aneuploidy. Prenat Diagn. 2021;41(10):1276–1283.
- McKanna T, Ryan A, Krinshpun S, et al. Fetal fraction-based risk algorithm for non-invasive prenatal testing: screening for trisomies 13 and 18 and triploidy in women with low cell-free fetal DNA. Ultrasound Obstet Gynecol. 2019;53(1):73–79.
Medical Disclaimer: The tools and content provided here are for educational and reference purposes only. They are not intended to substitute for professional medical advice, diagnosis, or treatment. Clinical decisions should always be based on the comprehensive assessment of a qualified healthcare professional.