Breakpoint junction analysis for complex genomic rearrangements with the caldera volcano-like pattern.,Human Mutation

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Breakpoint junction analysis for complex genomic rearrangements with the caldera volcano-like pattern.
Human Mutation ( IF 3.3 ) Pub Date : 2020-09-09 , DOI: 10.1002/humu.24108
Tomoe Yanagishita _{1,

2} , Taichi Imaizumi _{2,

3} , Keiko Yamamoto-Shimojima ₂ , Tamami Yano ₄ , Nobuhiko Okamoto ₅ , Satoru Nagata ₁ , Toshiyuki Yamamoto _{1,

2,

3,

6}

Affiliation

Chromosomal triplications can be classified into recurrent and nonrecurrent triplications. Most of the nonrecurrent triplications are embedded in duplicated segments, and duplication‐inverted triplication–duplication (DUP–TRP/INV‐DUP) has been established as one of the mechanisms of triplication. This study aimed to reveal the underlying mechanism of the TRP–DUP–TRP pattern of chromosomal aberrations, in which the appearance of moving averages obtained through array‐based comparative genomic hybridization analysis is similar to the shadows of the caldera volcano‐like pattern, which were first identified in two patients with neurodevelopmental disabilities. For this purpose, whole‐genome sequencing using long‐read Nanopore sequencing was carried out to confirm breakpoint junctions. Custom array analysis and Sanger sequencing were also used to detect all breakpoint junctions. As a result, the TRP–DUP–TRP pattern consisted of only two patterns of breakpoint junctions in both patients. In patient 1, microhomologies were identified in breakpoint junctions. In patient 2, more complex architectures with insertional segments were identified. Thus, replication‐based mechanisms were considered as a mechanism of the TRP–DUP–TRP pattern.

中文翻译：

具有火山口火山样模式的复杂基因组重排的断点连接分析。

染色体三倍体可分为复发性三倍体和非复发性三倍体。大多数非复发性三倍体嵌入在重复片段中，重复-倒置三倍体-重复（DUP-TRP/INV-DUP）已被确立为三倍体的机制之一。本研究旨在揭示染色体畸变的 TRP-DUP-TRP 模式的潜在机制，其中通过基于阵列的比较基因组杂交分析获得的移动平均值的出现类似于火山口火山样模式的阴影，其最初在两名神经发育障碍患者中发现。为此，使用长读长纳米孔测序进行全基因组测序以确认断点连接。自定义阵列分析和 Sanger 测序也用于检测所有断点连接。结果，TRP-DUP-TRP 模式仅由两名患者的两种断点连接模式组成。在患者 1 中，在断点连接处确定了微同源性。在患者 2 中，确定了具有插入段的更复杂的结构。因此，基于复制的机制被认为是 TRP-DUP-TRP 模式的一种机制。

更新日期：2020-09-09

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