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

Background/Objective: Prenatal cytogenetic testing is essential for pregnancies at high risk of chromosomal abnormalities. While conventional karyotyping detects large aneuploidies and structural rearrangements (>5–10 Mb), chromosomal microarray analysis (CMA) identifies smaller copy number variants (CNVs), increasing diagnostic yield by approximately 5%. CMA is now recommended as the first-tier test for evaluating fetal structural anomalies detected by ultrasound. Method: From March 2023 to September 2024, 344 prenatal samples were analyzed 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. CNVs were interpreted using NxClinical v6.0 and curated databases including ClinVar, DECIPHER, OMIM, ClinGen, and others. Results were aligned to the GRCh37/hg19 reference genome. Results: Chromosomal abnormalities were identified in 57/344 cases (16.5%). Of these, 39 were numerical chromosomal anomalies and 18 were pathogenic or likely pathogenic CNVs. Notably, 11 CNVs (3.2%) were undetectable by conventional karyotyping, emphasizing the added value of CMA. Conclusion: CMA enhances prenatal diagnostic accuracy by detecting submicroscopic CNVs that are not visible with conventional methods, supporting its routine use in prenatal genetic evaluation.