Position effect, cryptic complexity, and direct gene disruption as disease mechanisms in de novo apparently balanced translocation cases

The majority of apparently balanced translocation (ABT) carriers are phenotypically normal. However, several mechanisms were proposed to underlie phenotypes in affected ABT cases. In the current study, whole-genome mate-pair sequencing (WG-MPS) followed by Sanger sequencing was applied to further characterize de novo ABTs in three affected individuals. WG-MPS precisely mapped all ABT breakpoints and revealed three possible underlying molecular mechanisms. Firstly, in a t(X;1) carrier with hearing loss, a highly skewed X-inactivation pattern was observed and the der(X) breakpoint mapped ~87kb upstream an X-linked deafness gene namely POU3F4, thus suggesting an underlying long-range position effect mechanism. Secondly, cryptic complexity and a chromothripsis rearrangement was identified in a t(6;7;8;12) carrier with intellectual disability. Two translocations and a heterozygous deletion disrupted SOX5; a dominant nervous system development gene previously reported in similar patients. Finally, a direct gene disruption mechanism was proposed in a t(4;9) carrier with dysmorphic facial features and speech delay. In this case, the der(9) breakpoint directly disrupted NFIB, a gene involved in lung maturation and development of the pons with important functions in main speech processes. To conclude, in contrast to familial ABT cases with identical rearrangements and discordant phenotypes, where translocations are considered coincidental, translocations seem to be associated with phenotype presentation in affected de novo ABT cases. In addition, this study highlights the importance of investigating both coding and non-coding regions to decipher the underlying pathogenic mechanisms in these patients, and supports the potential introduction of low coverage WG-MPS in the clinical investigation of de novo ABTs.绝大多数外观平衡易位（apparently balanced translocation, ABT）携带者表型正常。然而，已有多项机制被提出用以阐释受累外观平衡易位患者的表型异常。本研究采用全基因组mate-pair测序（whole-genome mate-pair sequencing, WG-MPS）联合桑格测序（Sanger sequencing），对3名受累个体的新发（de novo）外观平衡易位样本进行了深入表征。全基因组mate-pair测序精准定位了所有外观平衡易位的断裂位点，并揭示了三种潜在的分子机制。首先，在1例伴听力损失的t(X;1)易位携带者中，我们观察到显著偏倚的X染色体失活模式，且衍生X染色体（der(X)）的断裂点定位于X连锁耳聋基因POU3F4上游约87kb处，提示存在长距离位置效应的潜在致病机制。其次，在1例伴智力障碍的t(6;7;8;12)易位携带者中，我们发现了隐匿性复杂重排与染色体碎裂（chromothripsis）重排。两处易位与一处杂合缺失破坏了SOX5基因——该基因为神经系统发育显性调控基因，此前在同类患者中已有报道。最后，在1例伴面部畸形与言语发育迟缓的t(4;9)易位携带者中，我们提出了直接基因破坏的致病机制。该病例中，衍生9号染色体（der(9)）的断裂点直接破坏了NFIB基因——该基因参与肺成熟与脑桥发育，且在主要言语过程中发挥重要功能。综上，与携带相同重排但表型不一致的家族性外观平衡易位病例（此类病例中的易位被认为是偶然事件）不同，受累的新发外观平衡易位患者的表型表现似乎与易位存在关联。此外，本研究强调了同时检测编码区与非编码区的重要性，以阐明此类患者的潜在致病机制，并支持将低覆盖度全基因组mate-pair测序应用于新发外观平衡易位的临床检测工作中。