Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency.
Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency.
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DOI：
10.1055/s-0042-1749345
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发表时间：
2022-08
影响因子：
6.7
通讯作者：
Sanchis-Juan, Alba
中科院分区：
文献类型：
--
作者：
De La Morena-Barrio, Belen;Stephens, Jonathan;Eugenia De La Morena-Barrio, Maria;Stefanucci, Luca;Padilla, Jose;Minano, Antonia;Gleadall, Nicholas;Luis Garcia, Juan;Fernanda Lopez-Fernandez, Maria;Morange, Pierre-Emmanuel;Puurunen, Marja;Undas, Anetta;Vidal, Francisco;Raymond, Frances Lucy;Vicente, Vicente;Ouwehand, Willem H.;Corral, Javier;Sanchis-Juan, Alba
遗传性抗凝血酶缺乏症（ATD）的鉴定对于预防可能危及生命的血栓形成事件至关重要。在高达70%的病例中鉴定出SERPINC 1的因果变异，大多数是单核苷酸变异和indel。由于SERPINC 1中大量的重复元件，ATD中结构变体（SV）的检测和表征仍然具有挑战性。在这里，我们对10个家族性和9个单例I型ATD病例进行了长读全基因组测序，这些病例通过功能和抗原检测得到证实，这些病例是从340名患有这种罕见疾病的患者中选出的，因为遗传分析要么是阴性的，要么是模糊的，要么是没有完全特征的。我们开发了一个分析工作流程来识别疾病相关SV。这种方法解决了，独立于其大小或类型，所有8个SV检测多个连接依赖性探针扩增，并确定了第一次复杂的重排以前被误分类为缺失。值得注意的是，我们确定了解释ATD的机制，在11例以前未知的缺陷：插入一个新的2.4 kb的SINE-VNTR-Alu逆转录元件，其特征在于从头组装和验证的特定聚合酶链反应扩增和测序的先证者和受影响的亲属。所有SV实现的核苷酸水平分辨率允许断点分析，其揭示了支持所有SV的共同的基于复制的机制的重复元件和微同源性。我们的研究强调了长读测序技术作为一种补充方法的实用性，以识别，表征和揭示参与ATD的致病SV的分子机制，并扩大了逆转录转座子插入引起的遗传疾病的目录。
The identification of inherited antithrombin deficiency (ATD) is critical to prevent potentially life-threatening thrombotic events. Causal variants in SERPINC1 are identified for up to 70% of cases, the majority being single-nucleotide variants and indels. The detection and characterization of structural variants (SVs) in ATD remain challenging due to the high number of repetitive elements in SERPINC1 . Here, we performed long-read whole-genome sequencing on 10 familial and 9 singleton cases with type I ATD proven by functional and antigen assays, who were selected from a cohort of 340 patients with this rare disorder because genetic analyses were either negative, ambiguous, or not fully characterized. We developed an analysis workflow to identify disease-associated SVs. This approach resolved, independently of its size or type, all eight SVs detected by multiple ligation-dependent probe amplification, and identified for the first time a complex rearrangement previously misclassified as a deletion. Remarkably, we identified the mechanism explaining ATD in 2 out of 11 cases with previous unknown defect: the insertion of a novel 2.4 kb SINE-VNTR-Alu retroelement, which was characterized by de novo assembly and verified by specific polymerase chain reaction amplification and sequencing in the probands and affected relatives. The nucleotide-level resolution achieved for all SVs allowed breakpoint analysis, which revealed repetitive elements and microhomologies supporting a common replication-based mechanism for all the SVs. Our study underscores the utility of long-read sequencing technology as a complementary method to identify, characterize, and unveil the molecular mechanism of disease-causing SVs involved in ATD, and enlarges the catalogue of genetic disorders caused by retrotransposon insertions.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
4.5
作者：
de Koning AP;Gu W;Castoe TA;Batzer MA;Pollock DD
通讯作者：
Pollock DD
影响因子：
4.9
作者：
Hancks DC;Kazazian HH Jr
通讯作者：
Kazazian HH Jr
影响因子：
10.4
作者：
de la Morena-Barrio, M. E.;Martinez-Martinez, I.;Vicente, V.
通讯作者：
Vicente, V.
影响因子：
5.3
作者：
Picard, Veronique;Chen, Jian-Min;Alhenc-Gelas, Martine
通讯作者：
Alhenc-Gelas, Martine