Optical genome mapping identifies cryptic balanced chromosomal rearrangements in karyotypically normal couples with recurrent pregnancy loss or adverse pregnancy history.

Recurrent pregnancy loss affects 1%-2% of reproductive-aged couples, with chromosomal abnormalities accounting for 40%-60% of cases. There is a close link between adverse pregnancy history (APH) and recurrent pregnancy loss (RPL). However, cryptic balanced translocations with translocated fragments smaller than the resolution of karyotyping or with similar banding patterns are often missed. This study, based on the testing results of 586 families who underwent preimplantation genetic testing for aneuploidy (PGT-A) due to RPL or APH, identified cryptic balanced translocations that were not detectable by conventional karyotyping, and validated them using Optical Genome Mapping (OGM). The prevalence of cryptic balanced translocations in the overall RPL/APH cohort was 1.19% (7/586, 95% CI: 0.58%-2.45%, Wilson score). It determined the incidence of cryptic balanced translocations in RPL or APH and changed the clinical management of these patients. Additionally, OGM resolved a 4-chromosome complex chromosomal rearrangement (CCR) involving 6 breakpoints and elucidated the genetic basis of two whole-exome sequencing-negative monogenic disorders by demonstrating pathogenic disruptions of EXT1 and PITX2 genes. OGM can be used as a second-line diagnostic tool, in addition to karyotype analysis and CNV-seq, for etiological screening of couples with recurrent pregnancy loss and adverse pregnancy history. The main conclusion of this study is that OGM can identify cryptic structural rearrangements, thereby enabling timely conversion of clinical management from PGT-A to preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR), and facilitating the transfer of euploid, non-carrier embryos for couples with RPL or APH.