Nanopore Sequencing with T2T-CHM13 for Accurate Detection and Blocking of Structural Rearrangements in Highly Repetitive Heterochromatin Regions in Human Embryos

Abstract Background Structural rearrangements in highly repetitive heterochromatin regions can result in miscarriage or fetal malformations, but detecting and blocking these rearrangements has been challenging. Recently, the completion of a complete human genome (T2T-CHM13) has made it possible to accurately characterize structural rearrangements in these regions. Results We developed a methodology based on T2T-CHM13 and nanopore sequencing to detect and block structural rearrangements in highly repetitive heterochromatin. To validate this approach, we used nanopore sequencing on families with inversions and reciprocal translocations close to the centromere. With the T2T-CHM13 reference, we accurately detected the inversion and translocation in centromeres, constructed haplotypes, and prevented the transmission of structural rearrangements in offspring. Conclusions This study represents the first successful application of T2T-CHM13 in human reproduction and provides a feasible protocol for detecting and blocking structural rearrangements in heterochromatin in embryos.