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Case Reports
. 2023 Mar 4;23(1):104.
doi: 10.1186/s12887-023-03872-y.

A mosaic karyotype of 45,X/46,X,psu idic(Y)(q12) in a ten-year-old boy: integrating high-throughput sequencing with cytogenetic technique for precise diagnosis and genetic counselling

Hui Yin #  1 , Hua Xie #  2 , Jizhen Zou  3 , Xue Ye  1 , Ying Liu  1 , Cai He  3 , Shaofang Shangguan  2 , Haoran Liu  2 , Xiaoli Chen  4 , Xiaobo Chen  5
Affiliations
Case Reports

A mosaic karyotype of 45,X/46,X,psu idic(Y)(q12) in a ten-year-old boy: integrating high-throughput sequencing with cytogenetic technique for precise diagnosis and genetic counselling

Hui Yin et al. BMC Pediatr. .

Abstract

Background: Isodicentric Y chromosome (idic(Y)) is the most commonly reported aberration of the human Y chromosome, which is an important cause of abnormal sexual development. The breakpoints of isodicentric Y chromosome mostly occurred in Yq11.2 and Yp11.3, however, the breakpoints in Yq12 are relatively rare.

Case presentation: We described a 10-year-old boy presenting hypospadias, micropenis and short stature, as well as unilateral cryptorchidism without normal testicular seminiferous tubules structure by biopsy. Whole exome sequencing didn't find any pathogenic/likely pathogenic variants related to phenotypes of this patient. Copy number variation sequencing showed the duplication of whole Y chromosome. Subsequently, karyotyping and FISH analyses demonstrated his genetic diagnosis was mosaic 45,X[8]/46,X,psu idic(Y)(q12)[32], with the breakpoint in Yq12.

Conclusions: Our case proved that it would be beneficial to integrate high-throughput sequencing with cytogenetic technique for precise diagnosis, treatment and genetic counselling.

Keywords: Genetic counselling; High-throughput sequencing; Isodicentric Y chromosome; Mosaicism; Precise diagnosis.

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Conflict of interest statement

The authors have no conflicts of interest to declare.

Figures

Fig. 1
Fig. 1
Testicular biopsy with immature testicular (A) and epididymal (B)
Fig. 2
Fig. 2
The results of CNV-Seq. A CNV-Seq analyses for all the chromosomes. B CNV-Seq analyses for Y chromosome
Fig. 3
Fig. 3
The karyotype (A–C), metaphase FISH analyses (D–I) for the patient, and diagram of Y chromosome (J, K). D-F FISH signals on cell line of 46,X,idic(Y) karyotype. D SRY shown two red signals and DXZ1 shown only one green signal, respectively. E Two red DYZ3 signals revealed the inactive Y centromere and one red signal revealed the active Y centromere. F DYZ1 signal (red) presenting Yq12 heterochromatin shown minor and near the region of the Yq11.23 G-I FISH signals on cell line of 45,X karyotype. G Only one DXZ1(green) signal. H, I No DYZ3 or DYZ1 signal was observed, respectively. J Diagram of a normal Y chromosome. K Diagram of a isodicentric Y chromosome idic(Y)(q12). The breakpoint (arrow) is located in Yq12 (long arm), with a duplication of short arm, centromere, and proximal long arm and deletion of most part of Yq12 material
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