Comparison of four different detection techniques on copy number variations in preimplantation genetic testing: a retrospective study

Abstract Background: We aimed to explore the distinctions among four different methods for copy number variations (CNVs) detection, while also striving to identify the most optimal detection method tailored to CNVs of varying sizes. Methods: To investigate the detection rates and accuracy of four different CNVs testing techniques, we analysed the archived data from 16 couples undergoing PGT at the Reproductive Medical Center of the First Affiliated Hospital of Anhui Medical University from 2021 to 2023. All couples carried CNVs between one or both partners. Results: In this study, the detection rates of the four methods were comparable. In contrast, our findings revealed a significant difference in the rates of blastocysts failing quality control among the four methods (P=0.034). Additionally, the rates of undetermined blastocysts from low-coverage whole-genome sequencing (lc-WGS) at 1 Mb and 4 Mb resolution were notably higher than those in the other groups, although the statistical differences were not significant (P=0.078). Moreover, no significant differences were observed in the success rates of embryo transfer. Conclusion: Multiplex PCR sequencing of target SNP loci is limited to detecting the target region and cannot identify CNVs outside that specific region. Regardless of cost, whole-genome SNP genotyping is the recommended method for kilobase-level CNVs. In addition, for CNVs ranging from 1–4 Mb, low-coverage WGS is anticipated to be the optimal choice in the future. We believe that our study will inform on the subsequent provision of diverse PGT approaches for patients with different CNVs.