Computational methods for detecting patterns of complex genomic variation

项目摘要 结构变异（SV）-涉及拷贝数、倒位、易位和其他基因的变化。 机制-是遗传变异的重要来源。它们发生在生殖细胞系中，也发生在 matic细胞，它们有时在疾病中发挥巨大作用，癌症就是一个突出的例子。 在确定和编目“简单”变异，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， 其特征在于涉及多个断点和简单SV事件的广泛结构变化。在 以前的研究资助的赠款（17出版物），我们开发和扩展的工具，以确定 包括断裂融合桥在内的复杂SV，其特征在于特定的拷贝数模式， 不同基因组片段的链的分离，如Chromothripsis和Chromothripsis所定义的，以及病毒 介导的重排。也许与目前的建议最相关的是确定 较小（<10 Mb）基因组片段的局部扩增的结构和起源。与col- 在实验室中，我们观察到大量的大型环状染色体外DNA（Turner，Nature 2017）， 在众多组织学亚型的所有癌症样本中，有40%检测到它们。EcDNA很热- 复杂的，甚至是多染色体基因组重排的点，以及更多的机械解释 局部放大。这些发现得到了许多计算工具的发展的支持： AmpliconArchitect（AA），用于使用Illumina短读段重建ecDNA的精细结构， ViFi用于识别由于病毒在人体内整合而引起的复杂变异，ecDetect用于检测 以及在中期获得的细胞遗传学图像中定量ecDNA。为了获得这笔赠款，我们将（i） 开发扩增子重建器（AR）作为使用长链扩增子来消除AA重建扩增子歧义的工具。 reads-Oxford Nanopore，Paci fic Biosciences和Optical Nanopore技术;（ii）使用AR来理解 在实验室中通过ecDNA的定向进化来进化复杂的结构变异;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， 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.