The Diagnostic Utility of Prenatal Microarray in High-Risk Pregnancies: A Single-Center Experience in Enhancing Reproductive Care and Risk Stratification

Background/Objective: Prenatal cytogenetic testing is essential for pregnant women who are at high risk of having a child with a chromosomal abnormality. While conventional karyotyping detects large aneuploidies and structural rearrangements (>5–10 Mb), chromosomal microarray analysis (CMA) identifies smaller copy number variants (CNVs), increasing the diagnostic yield by approximately 5%. CMA is now recommended as the first-line test for evaluating fetal structural anomalies that are detected by ultrasound. Method: From March 2023 to September 2024, we analyzed 344 prenatal samples using conventional karyotyping and SNP-based CMA. Karyotyping was performed via flask culture, and CMA was conducted using the Infinium Global Screening Array Cyto (GSA-Cyto) on the Illumina iScan platform. We interpreted the CNVs using NxClinical v6.0 and curated databases including ClinVar, DECIPHER, OMIM, and ClinGen, among others. Our results aligned with the GRCh37/hg19 reference genome. Results: Chromosomal abnormalities were identified in 57/344 cases (16.5%). Of these, 39 cases were numerical chromosomal anomalies, and 18 cases were pathogenic or likely pathogenic CNVs. Notably, 11 CNVs (3.2%) were undetectable by conventional karyotyping, emphasizing the added value of CMA. Conclusions: CMA enhances the prenatal diagnostic accuracy by detecting submicroscopic CNVs that are not visible with conventional methods, supporting the routine use of this analysis in prenatal genetic evaluation.