TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data

Meng, Guofeng; Tan, Ying; Fan, Yue; Wang, Yan; Yang, Guang; Fanning, Gregory; Qiu, Yang

doi:10.1534/g3.118.200900

Cited by 16 publications

(12 citation statements)

References 22 publications

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“…In this process, bedtools 35 was used by setting the minimum overlap as 5000 bp or the max length of loop anchors, and ensuring that there was zero gap. The self-contacted loops were filtered so that the anchoring regions of the same loops were not overlapped 36 .…”

Section: Methodsmentioning

confidence: 99%

Three-dimensional chromatin architecture datasets for aging and Alzheimer’s disease

Meng

et al. 2023

Sci Data

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Recently, increasing studies are indicating a close association between dysregulated enhancers and neurodegenerative diseases, such as Alzheimer’s disease (AD). However, their contributions were poorly defined for lacking direct links to disease genes. To bridge this gap, we presented the Hi-C datasets of 4 AD patients, 4 dementia-free aged and 3 young subjects, including 30 billion reads. As applications, we utilized them to link the AD risk SNPs and dysregulated epigenetic marks to the target genes. Combining with epigenetic data, we observed more detailed interactions among regulatory regions and found that many known AD risk genes were under long-distance promoter-enhancer interactions. For future AD and aging studies, our datasets provide a reference landscape to better interpret findings of association and epigenetic studies for AD and aging process.

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Section: Methodsmentioning

confidence: 99%

Three-dimensional chromatin architecture datasets for aging and Alzheimer’s disease

Meng

et al. 2023

Sci Data

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“…The cleaned and corrected reads were mapped with HBV A genotype by BLAST to obtain HBV containing reads. TSD software (Meng et al, 2019) was used to analysis the HBV integration site and hg19 was used as the reference genome. The genes around 100 kb upstream and downstream of the HBV integration site were searched on the NCBI website (https://www.ncbi.nlm.nih.gov/).…”

Section: Methodsmentioning

confidence: 99%

Pacbio Sequencing of PLC/PRF/5 Cell Line and Clearance of HBV Integration Through CRISPR/Cas-9 System

Chen

Guan

et al. 2021

Front. Mol. Biosci.

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The integration of HBV DNA is one of the carcinogenic mechanisms of HBV. The clearance of HBV integration in hepatocyte is of great significance to cure chronic HBV infection and thereby prevent the occurrence of HBV-related hepatocellular carcinoma (HCC). However, the low throughput of traditional methods, such as Alu-PCR, results in low detecting sensitivity of HBV integration. Although the second-generation sequencing can obtain a large amount of sequencing data, but the sequencing fragments are extremely short, so it cannot fully explore the characteristics of HBV integration. In this study, we used the third-generation sequencing technology owning advantages both in sequencing length and in sequencing depth to analyze the HBV integration characteristics in PLC/PRF/5 cells comprehensively. A total of 4,142,311 cleaning reads was obtained, with an average length of 18,775.6 bp, of which 84 reads were fusion fragments of the HBV DNA and human genome. These 84 fragments located in seven chromosomes, including chr3, chr4, chr8, chr12, chr13, chr16, and chr17. We observed lots of DNA rearrangement both in the human genome and in HBV DNA fragments surrounding the HBV integration site, indicating the genome instability causing by HBV integration. By analyzing HBV integrated fragments of PLC/PRF/5 cells that can potentially express HBsAg, we selected three combinations of sgRNAs targeting the integrated fragments to knock them out with CRISPR/Cas9 system. We found that the sgRNA combinations could significantly decrease the level of HBsAg in the supernatant of PLC/PRF/5 cells, while accelerated cell proliferation. This study proved the effectiveness of third-generation sequencing to detect HBV integration, and provide a potential strategy to reach HBsAg clearance for chronic HBV infection patients, but the knock-out of HBV integration from human genome by CRISPR/Cas9 system may have a potential of carcinogenic risk.

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“…For instance, the HepG2.2.15 cell line may contain at most five integrations, 21 and the PLC/PRF/5 cell line had nine integration regions reported. 23 Among the cell populations of the infected liver, it is estimated that there is about 1 integration per 10 3 ∼10 4 cells according to observations in an in vitro infection model. 8 Therefore, it requires detection methods that have adequate sensitivity to identify such limited events in bulk tissue samples.…”

Section: Hbv Integration Detection: Hybridization Cloning Amplification and Next-generation Sequencing (Ngs) Solutionsmentioning

confidence: 99%

“…To meet the requirement for the characterization of entire integrants, long-read sequencing, with the longest single read over 2 Mb, is able to directly read through the entire integration region. 23 It can not only reveal integrations affected by large structure variations within the host genome but also characterize the organization of multiple copies of HBV fragments within the same integration site. 23 …”

Section: Hbv Integration Detection: Hybridization Cloning Amplification and Next-generation Sequencing (Ngs) Solutionsmentioning

confidence: 99%

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HBV Integration Induces Complex Interactions between Host and Viral Genomic Functions at the Insertion Site

Zhang

Protzer

et al. 2021

Journal of Clinical and Translational Hepatology

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Hepatitis B virus (HBV), one of the well-known DNA oncogenic viruses, is the leading cause of hepatocellular carcinoma (HCC). In infected hepatocytes, HBV DNA can be integrated into the host genome through an insertional mutagenesis process inducing tumorigenesis. Dissection of the genomic features surrounding integration sites will deepen our understanding of mechanisms underlying integration. Moreover, the quantity and biological activity of integration sites may reflect the DNA damage within affected cells or the potential survival benefits they may confer. The well-known human genomic features include repeat elements, particular regions (such as telomeres), and frequently interrupted genes (e.g., telomerase reverse transcriptase [i.e. TERT ], lysine methyltransferase 2B [i.e. KMT2B ], cyclin E1 [ CCNE1 ], and cyclin A2 [ CCNA2 ]). Consequently, distinct genomic features within diverse integrations differentiate their biological functions. Meanwhile, accumulating evidence has shown that viral proteins produced by integrants may cause cell damage even after the suppression of HBV replication. The integration-derived gene products can also serve as tumor markers, promoting the development of novel therapeutic strategies for HCC. Viral integrants can be single copy or multiple copies of different fragments with complicated rearrangement, which warrants elucidation of the whole viral integrant arrangement in future studies. All of these considerations underlie an urgent need to develop novel methodology and technology for sequence characterization and function evaluation of integration events in chronic hepatitis B-associated disease progression by monitoring both host genomic features and viral integrants. This endeavor may also serve as a promising solution for evaluating the risk of tumorigenesis and as a companion diagnostic for designing therapeutic strategies targeting integration-related disease complications.

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TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data

Cited by 16 publications

References 22 publications

Three-dimensional chromatin architecture datasets for aging and Alzheimer’s disease

Three-dimensional chromatin architecture datasets for aging and Alzheimer’s disease

Pacbio Sequencing of PLC/PRF/5 Cell Line and Clearance of HBV Integration Through CRISPR/Cas-9 System

HBV Integration Induces Complex Interactions between Host and Viral Genomic Functions at the Insertion Site

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