Long‐read sequence analysis for clustered genomic copy number aberrations revealed architectures of intricately intertwined rearrangements

Abstract

Most chromosomal aberrations revealed by chromosomal microarray testing (CMA) are simple; however, very complex chromosomal structural rearrangements can also be found. Although the mechanism of structural rearrangements has been gradually revealed, not all mechanisms have been elucidated. We analyzed the breakpoint‐junctions (BJs) of two or more clustered copy number variations (CNVs) in the same chromosome arms to understand their conformation and the mechanism of complex structural rearrangements. Combining CMA with long‐read whole‐genome sequencing (WGS) analysis, we successfully determined all BJs for the clustered CNVs identified in four patients. Multiple CNVs were intricately intertwined with each other, and clustered CNVs in four patients were involved in global complex chromosomal rearrangements. The BJs of two clustered deletions identified in two patients showed microhomologies, and their characteristics were explained by chromothripsis. In contrast, the BJs in the other two patients, who showed clustered deletions and duplications, consisted of blunt‐end and nontemplated insertions. These findings could be explained only by alternative nonhomologous end‐joining, a mechanism related to polymerase theta. All the patients had at least one inverted segment. Three patients showed cryptic aberrations involving a disruption and a deletion/duplication, which were not detected by CMA but were first identified by WGS. This result suggested that complex rearrangements should be considered if clustered CNVs are observed in the same chromosome arms. Because CMA has potential limitations in genotype–phenotype correlation analysis, a more detailed analysis by whole genome examination is recommended in cases of suspected complex structural aberrations.

Xq22 deletion involving TCEAL1 in a female patient with early-onset neurological disease trait

“…These findings suggest end-joining mechanisms of double-strand break repair, nonhomologous end joining, and microhomology-mediated end joining. In the patient in this study, blunt-end fusion, believed to be a consequence of nonhomologous end joining, was detected, which is consistent with previous reports 12 .…”