Application of Trio-based Whole-Exome Sequencing in Fetal Ultrasound Anomalies: A Single-Center Retrospective Study of 454 Cases

Dongyi Yu^1,2,3*Dairong Feng^1,2,3Jiangbo Qu^1,2,3Lei Nie⁴Qian Liu⁵Lu Gao^1,2,3Wenzhen An⁵Na Liu^1,2,3Yuying Fang^1,2,3

• ¹Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong 250014, China, Jinan, China
• ²Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Jinan, Shandong 250014, China, Jinan, China
• ³Key Laboratory of Maternal & Fetal Medicine of the National Health Commission, Jinan, Shandong 250014, China, Jinan, China
• ⁴Medical Management Service Center of Health Commission of Shandong Province, Jinan, Shandong 250000, China, Jinan, China
• ⁵Medical Department, Zhejiang Biosan Biochemical Technologies Co., Ltd, 300 Fushan Street, Hangzhou, Zhejiang 310007, China, Hangzhou, China

This study assessed the diagnostic efficacy of trio-WES compared to CMA in fetuses with ultrasound anomalies and explored optimal prenatal testing strategies.A retrospective analysis included 454 fetuses undergoing trio-WES and/or CMA (2020-2023). Cases were classified into five categories and 19 subgroups based on ultrasound anomalies to evaluate diagnostic yields.Trio-WES achieved a diagnostic yield of 22.7% (103/454), surpassing CMA by 17.2% (78/454). Among the 103 positive cases, 73 (70.9%) involved single-nucleotide variants (SNVs) or small insertions/deletions (indels), 16 (15.5%) involved copy number variations (CNVs), 4 (3.9%) contained both SNVs/indels and CNVs, 9 (8.7%) were identified as aneuploidies, and 1 (1.0%) involved uniparental disomy. The diagnostic rates were highest for skeletal (39.2%) and multisystem anomalies (29.1%). Subgroup analysis revealed elevated yields for crystalline lens anomalies (60.0%) and cardiac rhabdomyoma (57.1%). Trio-WES clarified the mechanisms of ROH and enhanced the detection of imprinted gene-related disorders, preventing diagnostic oversights.Trio-WES significantly enhances prenatal diagnosis of ultrasound anomalies, offering incremental diagnostic value over CMA, particularly for skeletal/multisystem defects and specific structural subgroups. It elucidates ROH pathogenicity and aids imprinted disorder identification. Findings support integrating trio-WES into prenatal testing protocols for congenital malformations, providing a framework for clinical implementation.