What Are Fetal Fractions, and Why Are They Important?

During pregnancy, small fragments of fetal DNA circulate in the mother’s bloodstream. These DNA pieces, known as cell-free fetal DNA (cffDNA), provide valuable genetic information about the developing baby without requiring invasive procedures.

Fetal fraction refers to the proportion of this cffDNA relative to the total amount of cell-free DNA in maternal blood. Understanding its significance is crucial for ensuring accurate results in prenatal screening and detecting potential complications.

Role In Non-Invasive Prenatal Screening

Non-invasive prenatal screening (NIPS) has revolutionized the assessment of fetal genetic conditions, offering a safer alternative to procedures like amniocentesis and chorionic villus sampling. By analyzing cffDNA in maternal blood, NIPS can detect chromosomal abnormalities such as trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome) with high sensitivity and specificity. However, its accuracy depends on the fetal fraction—the proportion of cffDNA within the total circulating cell-free DNA. A low fetal fraction increases the risk of false negatives or inconclusive results.

Most laboratories require a minimum fetal fraction of 4% to 5% for reliable detection of chromosomal abnormalities. A 2019 study in Prenatal Diagnosis found that samples below this threshold had a significantly higher rate of no-call results, often necessitating repeat testing or alternative diagnostic approaches.

Fetal fraction also provides insights into potential pregnancy complications. Research has linked abnormally low levels to conditions such as fetal aneuploidy, placental insufficiency, and maternal obesity. A 2020 meta-analysis in The American Journal of Obstetrics and Gynecology found that pregnancies affected by trisomy 18 and trisomy 13 often exhibit lower fetal fractions. Additionally, high maternal body mass index (BMI) has been associated with reduced fetal fraction, likely due to increased maternal cfDNA diluting the fetal component.

Sources Of Cell-Free DNA

Cell-free DNA (cfDNA) in maternal blood comes from multiple sources, with the fetal component specifically derived from placental trophoblast cells. These short DNA fragments enter circulation through apoptosis, the programmed cell death involved in normal placental turnover. Unlike intact genomic DNA, cfDNA exists as fragmented double-stranded molecules, typically ranging from 50 to 300 base pairs in length.

Maternal cfDNA, which constitutes the majority of circulating DNA during pregnancy, originates from tissues such as leukocytes, endothelial cells, and adipocytes. Maternal leukocytes contribute significantly, particularly in conditions involving systemic inflammation or immune activation. This background DNA can obscure the fetal signal, making fetal fraction a critical factor in NIPS accuracy.

Both maternal and fetal cfDNA are rapidly degraded and eliminated from the bloodstream, primarily through the liver and kidneys. Research indicates that cfDNA has a short half-life, typically ranging from 30 minutes to a few hours. This rapid turnover ensures that cfDNA levels reflect real-time physiological conditions, though factors affecting DNA degradation—such as maternal kidney or liver dysfunction—could alter concentrations and impact fetal fraction measurements.

Methods Of Quantification

Accurately determining fetal fraction is essential for reliable NIPS, and several techniques have been developed for this purpose. One widely used approach measures DNA fragment size differences. Studies show that fetal-derived cfDNA fragments are generally shorter—around 140 base pairs—compared to maternal cfDNA. Advanced sequencing platforms analyze fragment length distributions to estimate fetal fraction.

Another method detects paternally inherited genetic markers absent from the maternal genome. Since fetal DNA contains both maternal and paternal alleles, identifying single nucleotide polymorphisms (SNPs) unique to the father allows bioinformatics algorithms to distinguish fetal DNA from maternal DNA. This SNP-based approach is particularly effective when the fetal genome carries distinct paternal contributions.

A third technique leverages DNA methylation patterns. Methylation, a biochemical modification that regulates gene expression, differs between placental and maternal tissues. Certain genomic regions exhibit fetal-specific methylation signatures, enabling targeted assays to selectively amplify and quantify fetal DNA. Some commercial NIPS platforms incorporate this method to enhance fetal fraction measurement.

Factors That Affect The Measurement

Several biological and technical factors influence fetal fraction measurement. One of the most significant is gestational age. Studies show that fetal fraction increases as pregnancy progresses, typically rising from around 3-4% in the first trimester to 10% or higher by the late second trimester. This increase is linked to placental growth and greater trophoblastic cell shedding. However, in some pregnancies, an unexpectedly low fetal fraction may indicate placental dysfunction or other anomalies.

Maternal characteristics also play a role. Higher maternal BMI is associated with a lower fetal fraction due to increased maternal cfDNA diluting the fetal component. A 2021 study in Clinical Chemistry found that for every 5-unit increase in BMI, fetal fraction decreased by approximately 0.6%.

Technical aspects of sample collection and processing further impact measurement accuracy. Delays in plasma separation after blood draw can lead to maternal white blood cell lysis, artificially elevating maternal cfDNA and lowering the fetal fraction. To mitigate this, clinical guidelines recommend processing samples within six hours and using specialized blood collection tubes to stabilize nucleated cells. Additionally, sequencing depth and bioinformatics algorithms influence measurement precision, with higher-resolution platforms providing more accurate estimates.

Clinical Insights

Beyond ensuring NIPS accuracy, fetal fraction offers insights into pregnancy health. Deviations from expected levels have been linked to complications such as fetal growth restriction, hypertensive disorders, and placental insufficiency. A lower-than-expected fetal fraction may indicate poor placental function, as trophoblast cells responsible for shedding fetal cfDNA also play a key role in maternal-fetal nutrient and oxygen exchange. Conversely, an unusually high fetal fraction has been observed in cases of confined placental mosaicism, where chromosomal abnormalities exist in placental cells but not in the fetus. This discrepancy can lead to misleading screening results.

Emerging research suggests fetal fraction could serve as an early biomarker for pregnancy complications such as preeclampsia. A 2022 study in BJOG: An International Journal of Obstetrics & Gynaecology found that pregnant individuals who later developed preeclampsia had significantly lower fetal fractions in the first trimester. While fetal fraction alone is not a diagnostic tool, integrating it with other biomarkers and ultrasound findings could improve prenatal risk assessment and maternal-fetal outcomes.