Comparative Efficacy of CNV-Sequencing and Karyotyping in Prenatal Genetic Diagnosis

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Abstract
Introduction: This study aimed to compare the efficacy of Copy Number Variation sequencing (CNV-Seq) with that of traditional karyotyping in prenatal diagnostics by assessing their concordance and ability to identify aneuploidies and structural abnormalities in fetal chromosomes. Methodology: We analyzed 177 amniotic fluid samples from pregnant women who were at or beyond 16 weeks of gestation, utilizing both CNV-Seq and karyotyping to evaluate their detection capabilities. Results: CNV-Seq identified chromosomal abnormalities in 46 cases (26.0%), demonstrating a higher detection rate compared to karyotyping, which found abnormalities in 40 cases (22.6%). CNV-Seq showed 100% concordance in identifying conditions such as trisomy 21, 18, 13, monosomy X, and 47, XXY. It also detected three mosaic cases and 13 copy number variations (CNVs) involving deletions or duplications that were not fully concordant with karyotyping results. Notably, CNV-Seq had a detection rate of 3.95% (7/177) for pathogenic or likely pathogenic chromosomal anomalies, and variants of uncertain significance (VUS) constituted 3.39% (6/177) of the findings. Conclusion: CNV-Seq improves the precision of prenatal diagnostics and broadens the scope for informed clinical decision-making, especially in managing pregnancies with detected abnormalities. The integration of CNV-Seq with traditional karyotyping addresses gaps in detection and supports a more comprehensive approach to prenatal care. Further studies should aim to include a broader and more diverse population to validate and expand upon these results.

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