Fetal Cell-free DNA Screening in Maternal Liquid Biopsies

Since the discovery of cell-free DNA (cfDNA) from the fetus in the peripheral blood of pregnant women and the associated development of non-invasive screening methods for frequent fetal chromosomal anomalies (Lo et al. and Chiu et al.), prenatal plasma cfDNA screening has been widely and successfully adopted. Unfortunately, pediatric patients and fetuses with numerous severe conditions associated with underlying single-gene defects often occur due to de novo monogenic variants that conventional prenatal plasma cfDNA screening or parental carrier screening cannot readily detect in maternal plasma samples (Yang et al. 2013, Yang et al. 2014, Petrovski et al., and Lord et al.).

In a study reported in Cell Discovery, researchers from China developed a prenatal cfDNA screening technique known as COATE-seq (coordinative allele-aware target enrichment sequencing) to support the concurrent screening of fetal monogenic and chromosomal conditions in liquid biopsies of maternal blood (Zhang et al. 2022). COATE-seq detects low-level fetal variants associated with common aneuploidies or copy number variations and simultaneously analyzes cfDNA fragment length and the allelic fraction associated with fetal monogenic variants. In their more recent Nature Medicine study (Zhang et al. 2025), the authors reported on a prospective, multicenter, and observational study of pregnant women at elevated risk for fetal genetic conditions, which aimed to evaluate the clinical validity and detection capabilities of prenatal screening using COATE-seq when targeting prevalent types of pathogenic genetic variants. Overall, the results of this exciting study demonstrated that cfDNA screening of maternal liquid biopsies represents a non-invasive and accurate means of identifying fetal pathogenic variants in high-risk pregnancies.

Active Motif is here to support your liquid biopsy-based studies, as highlighted by the recent release of RapCap (Rapid Capture) magnetic beads for the isolation of cfDNA. RapCap beads have revolutionized cfDNA isolation from blood plasma and saliva thanks to a simplified, column‐free workflow. Unlike traditional spin-column methods that rely on multiple centrifugation and binding steps, RapCap beads employ a surface engineered for high affinity to cfDNA, allowing rapid and efficient capture directly from plasma, saliva, or other patient samples isolated via liquid biopsies.

• The study enrolled and followed up 1,090 pregnant women (median age of 30.8 years) from three Chinese maternity hospitals
  • 876 fetal ultrasound anomalies, 116 abnormal maternal serum screening results, 86 high-risk results in standard cfDNA screening for chromosomal conditions, and 12 previous pregnancy history suggested an increased risk of fetal genetic conditions in these patients
• All participants underwent comprehensive prenatal cfDNA screening, including the analysis of 7 common aneuploidies, 7 microdeletions, and monogenic conditions associated with 75 genes
  • 978 pregnant women underwent invasive prenatal procedures (e.g., amniocentesis or chorionic villus sampling), while 112 participants were tested on products of conception or fetal cord blood to support a comparative analysis between cfDNA screening and other diagnostic tests
• Comprehensive cfDNA screening identified and diagnostic testing confirmed pathogenic genetic variants in 135 pregnancies - 89 aneuploidies, 9 microdeletions, and 37 monogenic variants (98.5% sensitivity and a 99.3% specificity relative to standard diagnostics)
• They detected diagnostic genetic variants in 98/876 fetuses with structural anomalies by ultrasound examination
  • 42 autosome and 13 sex chromosome aneuploidies, 6 microdeletions, and 37 monogenic conditions
  • Lymphatic/effusion anomalies had the highest overall detection rate for diagnostic genetic variants/chromosomal aberrations, while skeletal abnormalities had the highest diagnostic yield for monogenic conditions
• The detection rates of diagnostic genetic variants differed regarding fetal phenotypes/underlying genetic etiologies
  • 32.6% of fetuses with lymphatic/effusion abnormalities had chromosomal conditions (4.3% of cases caused by single-gene conditions), while 23.5% of fetuses with skeletal anomalies had monogenic conditions (1.2% of cases attributed to chromosomal abnormalities)
• 13/37 fetuses with structural anomalies caused by monogenic conditions possessed pathogenic variants in genes associated with postnatal neurological deficits even though affected fetuses lacked substantial central nervous system anomalies according to routine prenatal ultrasound screening
• The detection rate for diagnostic genetic variants increased by 60.7% for pregnancies with fetal structural anomalies when analyzing targeted monogenic conditions in conjunction with chromosomal conditions
• The study reported 623 live births, 268 elective abortions, and 2 spontaneous abortions in the 1090 participants followed up for 6 weeks after expected delivery dates (197 with no available pregnancy outcome data)
  • Of the 137 cases with positive results on diagnostic testing, 11 had live births, 106 had elective abortions, 1 had spontaneous abortion, and 19 had unknown pregnancy outcomes.
  • Among these cases, 100 had fetal anomalies on ultrasound screening (4 live births, 82 elective abortions, and 13 unknown pregnancy outcomes)
• The evaluation of pregnancy outcomes and postnatal and/or prenatal clinical examinations revealed no discrepancies between genetic diagnosis and clinical examination

Overall, this exciting liquid biopsy/cfDNA-focused study revealed how the analysis of maternal plasma samples employing COATE-seq could identify fetuses at risk of different genetic conditions by detecting genetic aberrations ranging from a single-nucleotide variant to whole chromosome copy number change. The authors state that the overall accuracy and substantially improved detection rate warrant further evaluations of prenatal cfDNA screening for the non-invasive evaluation of heterogeneous genetic condition risk in fetuses from maternal plasma samples.

For more on how cell-free DNA screening in maternal liquid biopsies via COATE-Seq can identify fetuses at risk of genetic conditions, see Nature Medicine, January 2024.

This article was originally published on the Active Motif blog.