Chromosomal insertions are thought to be rare structural rearrangements. The current understanding of the underlying mechanisms of their origin is still limited. In this study, we sequenced 16 cases with apparent simple insertions previously identified by karyotyping and/or chromosomal microarray analysis. Using mate-pair genome sequencing (GS), we identified all 16 insertions and revised previously designated karyotypes in 75.0% (12/16) of the cases. Additional cryptic rearrangements were identified in 68.8% of the cases (11/16). The incidence of additional cryptic rearrangements in chromosomal insertions was significantly higher compared to balanced translocations and inversions reported in other studies by GS. We characterized and classified the cryptic insertion rearrangements into four groups, which were not mutually exclusive: (1) insertion segments were fragmented and their subsegments rearranged and clustered at the insertion site (10/16, 62.5%); (2) one or more cryptic subsegments were not inserted into the insertion site (5/16, 31.3%); (3) segments of the acceptor chromosome were scattered and rejoined with the insertion segments (2/16, 12.5%); and (4) copy number gains were identified in the flanking regions of the insertion site (2/16, 12.5%). In addition to the observation of these chromothripsis- or chromoanasynthesis-like events, breakpoint sequence analysis revealed microhomology to be the predominant feature. However, no significant correlation was found between the number of cryptic rearrangements and the size of the insertion. Overall, our study provide molecular characterization of karyotypically apparent simple insertions, demonstrate previously underappreciated complexities, and evidence that chromosomal insertions are likely formed by nonhomologous end joining and/or microhomology-mediated replication-based DNA repair.

染色体插入被认为是罕见的结构重排。目前对它们起源的潜在机制的理解仍然有限。在这项研究中，我们对16个病例进行了测序，这些病例先前已通过核型分析和/或染色体微阵列分析确定了明显的简单插入。使用伴侣对基因组测序（GS），我们鉴定了所有16个插入片段，并在75.0％（12/16）的病例中修订了先前指定的核型。在68.8％的病例中发现了其他神秘的重排（11/16）。与GS在其他研究中报道的平衡易位和倒位相比，染色体插入中其他隐性重排的发生率明显更高。我们将隐含插入重排特征化并分为四类，这四类并非互斥的：（1）插入片段被片段化，其子片段重新排列并聚集在插入位置（10 / 16，62.5％）；（2）一个或多个隐性子段未插入插入位点（5 / 16，31.3％）；（3）受体染色体的各部分散开并与插入部分重新结合（2 / 16，12.5％）；（4）在插入位点的侧翼区域（2 / 16，12.5％）鉴定出拷贝数增加。除了观察到这些类似拟除染色体或拟染色体合成的事件外，断点序列分析还显示微同源性是主要特征。但是，在密码重排的数目和插入的大小之间没有发现显着的相关性。总体而言，我们的研究提供了核型明显插入的分子表征，