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 speci?c copy number patterns, detec- tion of chains of disparate genomic segments as de?ned 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 ampli?cation 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 ampli?cations. These discoveries were supported by the devlopment of many computational tools: AmpliconArchitect (AA) for reconstructing the ?ne structure of ecDNA using Illumina short-reads, ViFi for identifying complex variation due to viral integration in humans, and ecDetect for detection and quanti?cation 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, Paci?c 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.
The proposed project aims to study `complex' structural variation in genomes, characterized by extensive structural changes involving multiple breaaks and rearrangeements of the genome. Speci?cally, the PIs will characterize the structure, evolution, and function of extrachromosomal DNA and analyze their role in focal ampli?cation of genomic regions. The discoveries from the proposal could lead to novel ways of understanding and diagnosing cancer, and other diseases mediated by focal gene ampli?cation.
|Nguyen, Nam-Phuong D; Deshpande, Viraj; Luebeck, Jens et al. (2018) ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res 46:3309-3325|
|Akbari, Ali; Vitti, Joseph J; Iranmehr, Arya et al. (2018) Identifying the favored mutation in a positive selective sweep. Nat Methods 15:279-282|
|Beyter, Doruk; Lin, Miin S; Yu, Yanbao et al. (2018) ProteoStorm: An Ultrafast Metaproteomics Database Search Framework. Cell Syst 7:463-467.e6|
|Bakhtiari, Mehrdad; Shleizer-Burko, Sharona; Gymrek, Melissa et al. (2018) Targeted genotyping of variable number tandem repeats with adVNTR. Genome Res 28:1709-1719|
|Azad, Priti; Stobdan, Tsering; Zhou, Dan et al. (2017) High-altitude adaptation in humans: from genomics to integrative physiology. J Mol Med (Berl) 95:1269-1282|
|Chu, Wai Keung; Edge, Peter; Lee, Ho Suk et al. (2017) Ultraaccurate genome sequencing and haplotyping of single human cells. Proc Natl Acad Sci U S A 114:12512-12517|
|Stobdan, Tsering; Akbari, Ali; Azad, Priti et al. (2017) New Insights into the Genetic Basis of Monge's Disease and Adaptation to High-Altitude. Mol Biol Evol 34:3154-3168|
|Edge, Peter; Bafna, Vineet; Bansal, Vikas (2017) HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res 27:801-812|
|Cha, Seong Won; Bonissone, Stefano; Na, Seungjin et al. (2017) The Antibody Repertoire of Colorectal Cancer. Mol Cell Proteomics 16:2111-2124|
|Turner, Kristen M; Deshpande, Viraj; Beyter, Doruk et al. (2017) Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543:122-125|
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