Detection and genetic analysis of small supernumerary marker chromosomes in prenatal diagnosis

Introduction: Small supernumerary marker chromosomes (sSMCs) are small structurally abnormal chromosomes whose origin and structure are difficult to determine by conventional cytogenetic banding techniques. To analyze sSMCs discovered in prenatal diagnosis, explore the origin and clinical significance of fetal sSMCs, and inform genetic counseling and reproductive health care. Methods: Karyotyping was performed on pregnant women who underwent prenatal diagnosis in a Chinese hospital between April 2018 and April 2024. The sSMC cases encountered were further analyzed using copy number variation sequencing (CNV-seq) to determine the origin of the sSMCs and assess their clinical significance. Uniparental disomy (UPD) was excluded in the families with de novo sSMC cases using multiplex fluorescence PCR and capillary electrophoresis. Results: Out of 30,114 prenatal samples, 30 cases of sSMCs were identified, yielding a detection rate of 0.10%. Family analysis was performed on 23 of these cases, revealing 4 cases inherited and 19 cases of de novo mutations. CNV-seq was conducted on 27 cases, with 14 showing no abnormalities and 13 exhibiting copy number variations. Among the 10 cases where the origin of the sSMC was clearly identified, the duplications involved chromosomes 4, 10, 12, 15, 18, X, and Y, with pathogenic CNVs accounting for 70.0% (7/10) and variants of uncertain clinical significance accounting for 30.0% (3/10). Out of the 30 women with sSMCs detected, 13 chose to terminate the pregnancy, representing 43.3% (13/30). A follow-up was conducted on 13 de novo sSMC cases that were negative for CNV-seq. Among the live-born fetuses, all except one, who presented with speech delay, showed normal clinical features. UPD testing was successfully performed on 3 families (including the 3-year-old girl with speech delay), and all results were negative. Conclusions: Utilizing both karyotyping and molecular genetic testing is advantageous for effectively screening and identifying sSMCs. CNV-Seq is recommended as an important supplementary method for sSMC identification, thereby providing more detailed genetic counseling for prenatal diagnosis.