Combined optical genome mapping and cnv-seq identify complex Y-chromosome rearrangements and ectopy in 46,XX testicular disorder of sex development.

To define the genomic architecture of Y‑chromosome ectopy in a child with 46,XX testicular disorders of sex development (DSD) and illustrate the complementary roles of low‑coverage CNV sequencing (CNV‑seq) and optical genome mapping (OGM). A one‑and‑a‑half‑year‑old child with male phenotype, unfused scrotum, and hypospadias underwent clinical assessment and Doppler ultrasound, karyotyping, whole‑exome sequencing (WES), CNV‑seq, and OGM. CNV‑seq data were aligned to GRCh37; OGM maps were aligned to GRCh38 with T2T‑CHM13 consulted for Y display. Coordinates were harmonized for interpretation. FISH and long‑range PCR targeting the full SRY locus were not performed. Ultrasound showed bilateral scrotal testes, with no uterus or ovarian tissue. Karyotype was 46,XX, inv(9)(p12q13). CNV-seq identified called losses at Xp22.33 (287,328-3,605,487) and within Yp11.31-p11.2 (2,649,472-6,065,425) and Yp11.2 (7,270,527-9,599,178). OGM resolved a derivative X containing an insertion of Yp sequence at Xp22.33, with three re-join events in Yp11.2, including a deleted interval (~ 6.2-7.3 Mb) and a local inversion (~ 7.3-9.9 Mb); the call was ogm[GRCh38] der(X)(Ypter_Yp11.2::Yp11.2::Xp22.33_Xqter)(Ypter_6248448::9915169_7362950::3618476_Xqter). Harmonized coordinates indicate that the retained Yp11.3 interval includes SRY and is inserted into der(Xp22.33), supporting SRYpositive 46,XX testicular DSD on a coordinate basis. The Xp22.33 deletion supports counseling regarding SHOX haploinsufficiency-related growth surveillance. CNV-seq and OGM deliver nonredundant, genomewide dosage and architectural resolution that localizes the insertion site, defines breakpoint orientation, and provides counseling-relevant information beyond karyotype and WES. The coordinate-based inference of SRY and PAR1 involvement demonstrates a practical framework for integrating structural genomics into DSD diagnostics.