Application and insights of targeted next-generation sequencing in a large cohort of 46,XY disorders of sex development in Chinese

Abstract Purpose 46,XY disorders of sex development (46,XY DSD) are characterized by incomplete masculinization of genitalia with reduced androgenization. Accurate clinical management remains challenging, especially based solely on physical examination. Targeted next-generation sequencing (NGS) with known pathogenic genes provides a powerful tool for diagnosis efficiency. This study aims to identify the prevalent genetic variants by targeted NGS technology and investigate the diagnostic rate in a large cohort of 46,XY DSD patients, with most of them presenting atypical phenotypes. Methods Two different DSD panels were developed for sequencing purposes, targeting a cohort of 402 patients diagnosed with 46,XY DSD, who were recruited from the Department of Urology at Children’s Hospital, Zhejiang University School of Medicine (Hangzhou, China). The detailed clinical characteristics were evaluated, and peripheral blood was collected for targeted panels to find the patients’ variants. The clinical significance of these variants was annotated according to American College of Medical Genetics and Genomics (ACMG) guidelines. Results A total of 108 variants across 42 genes were found in 107 patients, including 46 pathogenic or likely pathogenic variants, with 45.7%(21/46) being novel. Among these genes, SRD5A2 , AR , FGFR1 , LHCGR , NR5A1 , CHD7 were the most frequently observed. Besides, we also detected some uncommon causative genes like SOS1 , and GNAS . Oligogenic variants were also identified in 9 patients, including several combinations PROKR2/FGFR1/CYP11B1 , PROKR2/ATRX , PROKR2/AR , FGFR1/LHCGR/POR , FGFR1/NR5A1 , GATA4/NR5A1 , WNT4/AR , MAP3K1/FOXL2 , WNT4/AR , and SOS1/FOXL2 . Conclusion The overall genetic diagnostic rate was 11.2%(45/402), with an additional 15.4% (62/402) having variants of uncertain significance. Additionally, trio/duo patients had a higher genetic diagnostic rate (13.4%) compared to singletons (8.6%), with a higher proportion of singletons (15.1%) presenting variants of uncertain significance. In conclusion, targeted gene panels identified pathogenic variants in a Chinese 46,XY DSD cohort, expanding the genetic understanding and providing evidence for known pathogenic genes’ involvement.