The genetic etiology of spontaneous abortion: insights from chromosomal microarray analysis and whole-exome sequencing.

Spontaneous abortion is one of the most common adverse pregnancy outcomes, with an incidence of approximately 15-25% in clinically recognized pregnancies. Chromosomal abnormalities are recognized as a primary genetic etiology, yet the specific underlying molecular mechanisms and pathways remain incompletely understood. Embryonic tissue samples from 1585 patients with spontaneous abortion were collected from January 2019 to June 2025. Chromosomal microarray analysis (CMA) was used for whole-genome detection of chromosomal abnormalities, including aneuploidy and copy number variations (CNVs). Functional enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted on CNV-related genes. 34 cases with negative CMA results and a history of recurrent pregnancy loss (≥ 2 episodes) were randomly selected to undergo whole-exome sequencing (WES) for the screening of monogenic variants. Statistical analysis included chi-square tests for inter-group comparisons, restricted cubic splines (RCS), and multivariate logistic regression for assessing risk factors. The detection rate of chromosomal abnormalities was 54.44%, mainly numerical abnormalities, with trisomy 16 and X monosomy being the most common subtypes. Structural variants include CNVs, loss of heterozygosity (LOH) and Runs of homozygosity(ROH). The results of the GO enrichment analysis indicated that genes associated with CNVs are primarily involved in hemostasis regulation and monocyte migration; KEGG enrichment analysis indicated that the Toll-like receptor signaling pathway and the neuroactive ligand-receptor interaction pathway may play a significant role in the pathogenesis of miscarriage. Multivariate Logistic regression analysis revealed that a mother's age of ≥ 35 years was an independent risk factor (OR = 1.72, 95%CI: 1.31-2.26), while a gestational age of ≥ 12 weeks had a protective effect (OR = 0.27, 95%CI: 0.21-0.34). The RCS model revealed a U-shaped relationship between maternal age and the risk of chromosomal abnormalities. The risk was lowest at ages 28-29 (OR = 0.99) and increased gradually after age 30; the risk of chromosomal abnormalities peaked between 8 and 10 weeks of gestation. The diagnostic yield of WES in recurrent miscarriage cases with normal CMA results reached 26.47%. This approach identified a variant in the MOS gene associated with oocyte maturation defects, along with clinically significant variants in possible miscarriage-implicated genes such as TTC7A. Chromosomal abnormalities, particularly trisomy 16 and monosomy X, along with dysregulation of hemostatic and immune pathways, are central to spontaneous abortion etiology. Advanced maternal age, defined as 30 years or older, and early gestational loss are key risk factors, challenging the conventional threshold of 35 years. The use of a combined CMA and WES strategy has effectively improved the genetic diagnosis rate, demonstrating the complementary value and advantages of combining chromosomal and single-gene testing technologies in diagnosing the causes of miscarriage.