Noninvasive Cell-Free DNA-Based Approach for the Diagnosis of Aneuploidies in Spontaneous Abortion

Spontaneous abortion is the most common complication in early pregnancy, with chromosomal abnormalities accounting for up to 50% of first-trimester losses. Conventional genetic analyses often rely on invasive procedures that may be limited by technical challenges and patient reluctance. This study aimed to evaluate the feasibility and diagnostic performance of cell-free DNA (cfDNA)-based testing as a noninvasive approach for detecting chromosomal abnormalities in first-trimester spontaneous abortion.

This retrospective observational study included pregnant individuals diagnosed with spontaneous abortion between 7 + 0 and 14 + 6 weeks of gestation from 2022 to 2025. cfDNA was extracted from maternal plasma and analyzed using the VeriSeq™ NIPT Solution v2 (Illumina). A subset of participants who underwent dilation and curettage (D&C) also had fetal tissue analyzed via chromosomal microarray analysis (CMA), which served as the reference standard. Primary outcomes included the rate of non-informative results (NIR), fetal fraction (FF) ≥4%, and detection rate of chromosomal abnormalities. Sensitivity, specificity, and predictive values of cfDNA were calculated relative to CMA.

A total of 299 participants underwent cfDNA testing, of whom 28 also had fetal tissue CMA. The mean FF was 5.83%, with 231/299 (77.3%) samples having FF ≥4%. NIR occurred in 6 cases (2.0%), while 62 (20.7%) had FF <4%. Among cfDNA results with FF ≥4%, 130/231 (56.3%) showed chromosomal abnormalities, with trisomy 16 being the most common. In the D&C subgroup, cfDNA and CMA results were fully concordant (sensitivity and specificity: 100%). FF was positively correlated with gestational age (r = 0.42, p < 0.001).

cfDNA-based testing represents a feasible and accurate noninvasive method for detecting chromosomal abnormalities following first-trimester pregnancy loss. It may offer an effective alternative to invasive genetic testing, particularly when tissue sampling is unavailable or declined. However, the retrospective design and the lack of detailed maternal clinical characteristics, including body mass index and other factors potentially influencing FF, represent important limitations that should be considered when interpreting these findings.