Chromoanagenesis is a genomic event responsible for the formation of complex structural chromosomal rearrangements (CCRs). Germline chromoanagenesis is rare and the majority of reported cases are associated with an affected phenotype. Here, we report a healthy female carrying two de novo CCRs involving chromosomes 4, 19, 21 and X and chromosomes 7 and 11, respectively, with a total of 137 breakpoint junctions (BPJs). We characterized the CCRs using a hybrid-sequencing approach, combining short-read sequencing, nanopore sequencing, and optical mapping. The results were validated using multiple cytogenetic methods, including fluorescence in situ hybridization, spectral karyotyping, and Sanger sequencing. We identified 137 BPJs, which to our knowledge is the highest number of reported breakpoint junctions in germline chromoanagenesis. We also performed a statistical assessment of the positioning of the breakpoints, revealing a significant enrichment of BPJ-affecting genes (96 intragenic BPJs, 26 genes, p < 0.0001), indicating that the CCRs formed during active transcription of these genes. In addition, we find that the DNA fragments are unevenly and non-randomly distributed across the derivative chromosomes indicating a multistep process of scattering and re-joining of DNA fragments. In summary, we report a new maximum number of BPJs (137) in germline chromoanagenesis. We also show that a hybrid sequencing approach is necessary for the correct characterization of complex CCRs. Through in-depth statistical assessment, it was found that the CCRs most likely was formed through an event resembling chromoplexy—a catastrophic event caused by erroneous transcription factor binding.

染色体发生是负责形成复杂结构染色体重排 (CCR) 的基因组事件。种系染色体发生是罕见的，大多数报告的病例与受影响的表型有关。在这里，我们报告了一名健康女性携带两个从头 CCR，分别涉及染色体 4、19、21 和 X 以及染色体 7 和 11，共有 137 个断点连接 (BPJ)。我们使用混合测序方法对 CCR 进行了表征，结合了短读长测序、纳米孔测序和光学图谱。使用多种细胞遗传学方法验证了结果，包括荧光原位杂交、光谱核型分析和 Sanger 测序。我们确定了 137 个 BPJ，据我们所知，这是生殖系染色体发生中报告的断点连接数最多的。p  < 0.0001），表明 CCR 在这些基因的活跃转录过程中形成。此外，我们发现 DNA 片段不均匀且非随机地分布在衍生染色体上，表明 DNA 片段的分散和重新连接的多步骤过程。总之，我们报告了生殖系染色体发生中新的最大数量的 BPJ (137)。我们还表明，混合测序方法对于复杂 CCR 的正确表征是必要的。通过深入的统计评估，发现 CCR 最有可能是通过类似于 chromoplexy 的事件形成的——一种由错误的转录因子结合引起的灾难性事件。