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.
摘要：
通过染色体微阵列测试（CMA）发现的大多数染色体畸变都很简单；但是，也可以发现非常复杂的染色体结构重排。尽管结构重排的机制已经逐渐显现出来,并非所有机制都已阐明。我们分析了同一染色体臂中两个或多个聚集的拷贝数变异（CNV）的断点连接（BJ），以了解它们的构象和复杂结构重排的机制。将CMA与长读数全基因组测序（WGS）分析相结合，我们成功地确定了4例患者的聚集CNV的所有BJ.多个CNVs彼此错综复杂地交织在一起，4例患者聚集的CNV参与了整体复杂的染色体重排。在两名患者中确定的两个聚集缺失的BJ显示微同源性，它们的特征由染色体解释。相比之下,另外两个病人的BJ,显示集群删除和重复的人，由钝端和非模板插入组成。这些发现只能通过替代的非同源末端连接来解释，与聚合酶theta有关的机制。所有患者至少有一个倒置段。三名患者表现出涉及破坏和缺失/重复的隐匿性畸变，CMA未检测到，但首次由WGS鉴定。该结果表明，如果在相同的染色体臂中观察到成簇的CNV，则应考虑复杂的重排。因为CMA在基因型-表型相关性分析中具有潜在的局限性,在怀疑复杂结构畸变的情况下，建议通过全基因组检查进行更详细的分析。
