Application of High-Throughput Sequencing Technology in Fetal Growth Restriction and Analysis of Pregnancy Outcomes

Fetal growth restriction (FGR) is a significant cause of perinatal morbidity and mortality. This study aimed to verify whether high-throughput sequencing technologies (Copy Number Variation Sequencing, CNV-seq; Trio Whole Exome Sequencing, Trio-WES) can overcome the limitations of traditional karyotype analysis and improve the detection rate of genetic etiologies in FGR fetuses, and to analyze associated pregnancy outcomes.

A retrospective analysis was conducted on 235 fetuses who underwent invasive prenatal diagnosis following ultrasound-diagnosed fetal growth restriction (FGR) at Liuzhou Maternal and Child Health Hospital between January 2019 and March 2025. All cases underwent concurrent chromosomal karyotyping and genome-wide copy number variation sequencing (CNV-seq). Among these, 19 cases with normal results from both karyotyping and CNV-seq were further analyzed using trio-whole exome sequencing (Trio-WES). For karyotyping and CNV-seq, genomic DNA was extracted from amniotic fluid or umbilical cord blood samples. For Trio-WES, genomic DNA was obtained from fetal amniotic fluid or umbilical cord blood, along with peripheral blood samples from both parents as controls.

Among the 235 FGR specimens, chromosomal abnormalities were detected in 9 cases (3.8%, 9/235) by karyotype analysis of chromosomes, and 26 cases (11.1%,26/235) by CNV-seq technology.Among FGR cases with normal karyotypes, CNV-seq detected an additional 17 abnormalities (7.5%, 17/226). When comparing the two techniques, the abnormal detection rate of CNV-seq technology was higher than that of karyotype analysis, and the difference was statistically significant (P < 0.05). Among the 19 cases negative for both karyotype and CNV-seq, Trio-WES detected 6 abnormalities (31.6%, 6/19), including 3 pathogenic variants, 1 likely pathogenic variant, and 2 variants of uncertain significance (VOUS). A total of 32 cases (13.6%, 32/235) of abnormal variations were detected by the combination of karyotype analysis and high-throughput sequencing. Pregnancy outcomes included: all 9 karyotype-abnormal cases chose termination of pregnancy (TOP); of the 17 CNV-seq-abnormal cases (karyotype-normal), 10 underwent TOP (3 with combined organ malformations) and 7 had live births (6 with normal follow-up to 2 years, 1 with developmental delay and hypertonia at 2-year follow-up); of the 6 Trio-WES-abnormal cases, 5underwent TOP and1 had live births (1 with normal follow-up).

Compared with traditional karyotype analysis (3.8% detection rate), high-throughput sequencing technologies (CNV-seq and Trio-WES) significantly improve the detection rate of genetic abnormalities in FGR fetuses to 13.6%. The "karyotype analysis + CNV-seq + Trio-WES" stepwise detection protocol provides critical support for prenatal genetic counseling and clinical decision-making,and contributes to optimizing pregnancy management and outcomes.