Analysis of complex constitutional genome rearrangements in patients with congenital defects

"Complex chromosomal rearrangements (CCRs) involving multiple breakpoints have been associated with congenital malformations. We analyzed the genomic structure of seven constitutional CCRs. We identified between 4 and 23 clustered breakpoint junctions per CCR leading to complex networks of inter- and intra-chromosomal rearrangements. We found that breakpoint junctions form closely spaced pairs on the reference genome indicating the occurrence of double-stranded DNA breaks. Breakpoint junction sequencing revealed small non-templated insertions, microhomology and many blunt fusions, which is in line with non-homologous end-joining (NHEJ) mediated assembly of chromosomal fragments. Deletions represent chromosomal segments that were not included in the chromosome reassembly process. These rearrangement characteristics are reminiscent of chromothripsis clusters described in cancer cells and are distinct from replicative mechanisms of DNA repair. We included data on two patients with rearrangements caused by template switching to outline the difference with chromothripsis rearrangements. Our data show that localized chromosome shattering by double-stranded breaks and subsequent repair by NHEJ is a major mechanism causing CCRs in the germline."