Computational methods for detecting patterns of complex genomic variation

项目摘要 结构变异(SVS)--涉及拷贝数、倒位、易位等方面的变化 机制--是遗传变异的重要来源。它们出现在生殖系中，也出现在- 马季奇细胞有时在疾病中扮演着非常重要的角色，癌症就是一个突出的例子。 在识别和编目“简单”变体方面做了大量工作，如删除、重复、 易位，以及其他。相比之下，我们继续提出的建议是关于“复杂的”结构变化， 以涉及多个断点和简单SV事件的广泛结构变化为特征。在……里面 在之前由赠款资助的研究(17篇出版物)中，我们开发和扩展了工具来确定 包括断裂融合桥在内的复杂SVS，其特征是fic拷贝数模式，检测- 不同的基因组节段链的连接，如由染色质和多染色质所致的defiNed，以及病毒 调解的重排。也许与当前提案最相关的是确定 较小(&lt；10Mb)基因组片段的焦点扩增fi的结构和来源。与科尔合作- 实验室，我们观察到了大量的大的圆形，染色体外的DNA(Turner，自然，2017)， 在许多组织亚型的所有癌症样本中检测到它们的40%。EcDNA很火爆- 斑点，复杂的，甚至多个染色体的基因组重排，和o↵er一个机械的解释 焦点放大fi阳离子。这些发现得到了许多计算工具的发展的支持： 扩增结构(AA)，用于使用Illumina短读来重建ecDNA的fiNe结构， ViFi用于识别由于病毒整合而在人类体内产生的复杂变异，ecDetect用于检测 中期细胞遗传学图像中ECDNA的定量fi阳离子。对于这笔赠款，我们将：(I) 开发扩增子重构器(AR)作为使用LONG来消除AA重构扩增歧义的工具 阅读-牛津纳米孔、Pacific生物科学和光学纳米孔技术；(Ii)使用AR来理解 通过实验室中ecDNA的定向进化来实现复杂结构变异的进化；以及(Iii)， 整合来自数千个全基因组序列、转录本和其他表观遗传学数据的数据以阐明 EcDNA元件的功能方面。

Project Summary Structural variations (SVs) – involving changes in copy number, inversions, translocations, and other mechanisms– are an important source of genetic variation. They occur in the germ-line and also in so- matic cells, where they sometimes play an outsized role in diseases, cancer being a prominent example. Much work has been done in identifying and cataloging `simple' variants such as deletions, duplications, translocations, and others. In contrast, our continuing proposal is about `complex' structural variation, characterized by extensive structural changes involving multiple breakpoints and simple SV events. In previous research funded by the grant (17 publications), we developed and extended tools for identifying complex SVs including Breakage Fusion Bridge characterized by specific copy number patterns, detec- tion of chains of disparate genomic segments as defined by Chromothripsis and Chromoplexy, and viral mediated rearrangements. Perhaps most relevant to the current proposal, is the problem of determining architecture and origin of focal amplification of smaller (< 10Mb) genomic segments. Working with col- laborators, we observed an abundance of large circular, extrachromosomal DNA (Turner, Nature 2017), detecting them in 40% of all cancer samples across a multitude of histological subtypes. EcDNA are hot- spots for complex, even multi-chromosomal genomic rearrangements, and o↵er a mechanistic explanation of focal amplifications. These discoveries were supported by the devlopment of many computational tools: AmpliconArchitect (AA) for reconstructing the fine structure of ecDNA using Illumina short-reads, ViFi for identifying complex variation due to viral integration in humans, and ecDetect for detection and quantification of ecDNA in cytogenetic images acquired in metaphase. For this grant, we will (i) develop Amplicon Reconstructor (AR) as a tool for disambiguated AA reconstructed amplicons using long reads–Oxford Nanopore, Pacific Biosciences, and Optical Nanopore technology; (ii) use AR to understand the evolution of complex structural variation thorugh directed evolution of ecDNA in the lab; and (iii), integrate data from thousands of whole genome sequences, transcript and other epigenetic data to elucidate the functional aspects of ecDNA elements.