Molecular characterization of ring chromosome 18 by low-coverage next generation sequencing.
Molecular characterization of ring chromosome 18 by low-coverage next generation sequencing.
复制标题
通过低覆盖率下一代测序对 18 号环染色体进行分子表征。
DOI：
10.1186/s12881-015-0206-x
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发表时间：
2015-07-30
影响因子：
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通讯作者：
Xu Z
中科院分区：
文献类型：
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作者：
Ji X;Liang D;Sun R;Liu C;Ma D;Wang Y;Hu P;Xu Z
环状染色体是一类结构异常的染色体，可导致严重的生长迟缓和其他临床缺陷。传统上，它们的诊断和鉴定在很大程度上依赖于传统的细胞遗传学和荧光原位杂交、基于阵列的比较基因组杂交和基于单核苷酸多态性阵列的比较基因组杂交。然而，这些方法在描述环状染色体结构方面效果不佳，并且只能提供低分辨率的断点图谱。在这里，我们将全基因组低覆盖率配对末端下一代测序(NGS)应用于两例疑似18号环染色体(r(18))，并描述了包括染色体剂量变化和断点连接在内的环结构。R(18)的断裂点和染色体拷贝数变异(CNV)以全基因组低复盖率配对末端NGS为特征。我们用单核苷酸多态芯片证实了剂量的变化，并用聚合酶链式反应和Sanger测序验证了连接位点区域。我们用NGS成功地完整地刻画了两个案例中的r(18)。我们以高分辨率绘制了断点，并识别了两种情况下的所有CNV。我们分析了断点区，发现两个断点位于重复序列区域内，两个断点位于重复序列区域附近。例2中的一个断裂点位于基因METTL4内，而其他断裂点是基因间的。我们证明了全基因组低覆盖率的成对末端NGS可以直接用于高分子分辨率的断裂点定位和检测r(18)上的所有CNV。这一方法将对r(18)上的基因型-表型相关性和环状染色体形成的潜在机制提供新的见解。我们的结果还表明，这可能是一种强有力的方法来诊断和表征临床上的环形染色体。本文的在线版本(doi：10.1186/s12881-0150206-x)包含补充材料，授权用户可以使用。
Ring chromosomes are one category of structurally abnormal chromosomes that can lead to severe growth retardation and other clinical defects. Traditionally, their diagnosis and characterization has largely relied on conventional cytogenetics and fluorescence in situ hybridization, array-based comparative genomic hybridization and single nucleotide polymorphism array-based comparative genomic hybridization. However, these methods are ineffectively at characterizing the ring chromosome structure and only offer a low resolution mapping of breakpoints. Here, we applied whole-genome low-coverage paired-end next generation sequencing (NGS) to two suspected cases of ring chromosome 18 (r(18)) and characterized the ring structure including the chromosome dosage changes and the breakpoint junction. The breakpoints and chromosome copy number variations (CNVs) of r(18) were characterized by whole-genome low-coverage paired-end NGS. We confirmed the dosage change by single nucleotide polymorphisms array, and validated the junction site regions using PCR followed by Sanger sequencing. We successfully and fully characterized the r(18) in two cases by NGS. We mapped the breakpoints with a high resolution and identified all CNVs in both cases. We analyzed the breakpoint regions and discovered two breakpoints located within repetitive sequence regions, and two near the repetitive sequence regions. One of the breakpoints in case 2 was located within the gene METTL4, while the other breakpoints were intergenic. We demonstrated that whole-genome low-coverage paired-end NGS can be used directly to map breakpoints with a high molecular resolution and detect all CNVs on r(18). This approach will provide new insights into the genotype-phenotype correlations on r(18) and the underlying mechanism of ring chromosomes formation. Our results also demonstrate that this can be a powerful approach for the diagnosis and characterization of ring chromosomes in the clinic. The online version of this article (doi:10.1186/s12881-015-0206-x) contains supplementary material, which is available to authorized users.