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Objective: To assess the value of next-generation sequencing-based copy number variation sequencing (CNV-seq) for the detection of copy number variations (CNVs) in prenatal diagnosis., Methods: The results of single nucleotide polymorphism array (SNP-array) for prenatal diagnosis from May 2018 to December 2020 were reviewed. Selected cases of CNVs of clinical significance or low-percentage mosaic aneuploidies were included. Preserved DNA samples of amniotic fluid DNA were detected by CNV-seq. The results of CNV-seq and CMA were analyzed., Results: A total of 16 488 data of SNP-array were re-analyzed, and 343 DNA samples were selected for the CNV-seq assay. All samples were successfully analyzed. Compared with the SNP-array, the proportion of full concordance, partial concordance and missed detection was 91.5% (314/343), 1.2% (4/343) and 7.3% (25/343), respectively. The non-detection zones of CNV-seq were confirmed, which have encompassed the SHOX gene and AZFc region., Conclusion: With a high accuracy and wide genome-wide coverage, CNV-seq is worthy for a wide application in prenatal diagnosis, though the limitation of testing should be taken into consideration, and the appropriate prenatal diagnosis method should be selected for different populations to reduce the occurrence of birth defects.