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

Background: 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. Methods: 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. Results: 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). Conclusion: 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. Keywords: fetal growth restriction, high-throughput sequencing, karyotype analysis of chromosomes, prenatal diagnosis, pregnancy outcome