An NGS-based approach to identify Y-chromosome variation in non-obstructive azoospermia

Copy number variations (CNVs), including deletions and duplications on the Y chromosome, are known genetic factors in azoospermia. Therefore, it is important to identify novel pathogenic CNVs related to azoospermia. In this study, we compared CNVs detected by STS-PCR and NGS in 107 individuals with nonobstructive azoospermia (NOA). STS-PCR analysis revealed that 8.14% (9/107) of patients had AZF deletions. The highest percentage of deletions was located in the AZFc region, followed by AZFa and AZFb+c. Positive CNVs, including four duplications, six deletions and three complex CNVs, were detected using NGS methods in 12.15% (13/107) of NOA patients. Both the duplications and deletions detected in q11.223 were confirmed to increase the genetic risk for NOA. A comparison between the STS-PCR results and NGS methods revealed concordant CNV-positive results in 4 of 107 cases (3.74%). The discrepancies included 6 cases with CNVs identified by NGS but not detected by STS-PCR, and two cases were detected by STS-PCR but not by NGS. Notably, four duplications were not identified and three complex CNVs were detected as simple deletions using STS-PCR analysis. The NGS method provides comprehensive results in detecting Y chromosome-linked CNVs, including deletions and duplications, which might broaden our understanding of NOA.