Isodicentric Y chromosome with multiple breakpoints in the pseudoautosomal region 1.

Isodicentric Y chromosomes are relatively common structural variants of the human genome. The underlying mechanism of isodicentric Y chromosomes with short arm breakpoints [idic(Yq)] remains to be clarified. We encountered a Japanese man with azoospermia and mild short stature. G-banding and array-based comparative genomic hybridization indicated that his karyotype was 45,X/46,X,idic(Y)(qter→p11.32::p11.32→qter) with a ~1.8 Mb terminal deletion. Whole genome sequencing suggested that the Y chromosome had four breakpoints in a ~7 kb region of the pseudoautosomal region 1 (PAR1). This case was assumed to have an idic(Yq) resulting from multiple DNA double-strand breaks in PAR1. This rearrangement may have been facilitated by the PAR1-specific chromatin architecture. The clinical features of the patient can be ascribed to SHOX haploinsufficiency and the presence of a 45,X cell line, although copy-number gains of some Yq genes and the size reduction of PAR1 may also contribute to his spermatogenic failure.

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