Prenatal diagnosis and genetic etiology of fetal skeletal dysplasia in China: a combined application of karyotyping, CNV-seq and WES

This study aimed to analyse the genetic causes of suspected skeletal dysplasia in Chinese fetuses by karyotyping, copy number variation sequencing (CNV-seq), and whole exome sequencing (WES), assessing the value of integrating these technologies in prenatal diagnosis. This study included singleton pregnancies with suspected skeletal malformations by prenatal ultrasound from January 2019 to December 2022. Fetal samples were obtained by amniocentesis or cordocentesis for karyotyping, CNV-seq, and WES analysis. The unmapped sequencing reads by CNV-seq were aligned to the pathogen database to detect intrauterine infection. The samples were stratified into lethal, intermediate, and non-lethal groups based on fetal condition severity assessed by ultrasonography. The overall molecular diagnostic yield was 45.95% (17/37). The detection rate for chromosomal abnormalities was 16.22% (6/37). WES further revealed an additional 11 cases with pathogenic or likely pathogenic (P/LP) variants in six genes, thereby increasing the diagnostic rate by 29.73% (11/37). Unmapped CNV-seq reads incidentally detected a congenital (CMV) infection in case 37, which was excluded from the severity-stratified analysis. When stratified by ultrasonographic severity, the diagnostic yield was highest in the lethal group (71.43%, 5/7), followed by the non-lethal (46.67%, 7/15) and intermediate groups (35.71%, 5/14), although the differences did not reach statistical significance ( P > 0.05). No live birth with normal development was observed among the molecularly confirmed lethal cases. The termination rate was approximately two-fold higher in the genetically positive group than in the negative group (52.94% vs. 26.67%). Novel findings included one rare case harboring two de novo COL2A1 variants in cis on the same allele and one novel de novo EHMT1 variant. This study underlines that Karyotyping, CNV-seq, and WES are complementary technologies for the prenatal diagnosis of fetal skeletal abnormalities. The combination of ultrasound-based stratification and molecular confirmation may improve risk assessment and inform reproductive decision-making.