ArticleG3 (Bethesda, Md.)2019
TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data.
Article in G3 (Bethesda, Md.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Development of a long-read high-throughput chromatin conformation capture method for evaluating bothbioRxiv : the preprint server for biology · 2025Article
- Development of an NGS-Based Estimation of Integrated HBV DNA in Liver Biopsies and Detection in Liquid Biopsies.Journal of medical virology · 2025Article
- Integrated DNA estimation in tissue biopsy and detection in liquid biopsy by HBV-targeted NGS assay.medRxiv : the preprint server for health sciences · 2024Article
- The role of the hepatitis B virus genome and its integration in the hepatocellular carcinoma.Frontiers in microbiology · 2024Review
- A survey of algorithms for the detection of genomic structural variants from long-read sequencing data.Nature methods · 2023Review
- Three-dimensional chromatin architecture datasets for aging and Alzheimer's disease.Scientific data · 2023Article
- Multiple HPV integration mode in the cell lines based on long-reads sequencing.Frontiers in microbiology · 2023Article
- Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture.Nature communications · 2021Article
- Long-read sequencing reveals the structural complexity of genomic integration of HBV DNA in hepatocellular carcinoma.NPJ genomic medicine · 2021Article
- Targeted Long-Read Sequencing Reveals Comprehensive Architecture, Burden, and Transcriptional Signatures from Hepatitis B Virus-Associated Integrations and Translocations in Hepatocellular Carcinoma Cell Lines.Journal of virology · 2021Article
- HBV Integration Induces Complex Interactions between Host and Viral Genomic Functions at the Insertion Site.Journal of clinical and translational hepatology · 2021Review
- Pacbio Sequencing of PLC/PRF/5 Cell Line and Clearance of HBV Integration Through CRISPR/Cas-9 System.Frontiers in molecular biosciences · 2021Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
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Authors and funding
7 authors.
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Abstract
PacBio sequencing is a powerful approach to study DNA or RNA sequences in a longer scope. It is especially useful in exploring the complex structural variants generated by random integration or multiple rearrangement of endogenous or exogenous sequences. Here, we present a tool, TSD, for complex structural variant discovery using PacBio targeted sequencing data. It allows researchers to identify and visualize the genomic structures of targeted sequences by unlimited splitting, alignment and assembly of long PacBio reads. Application to the sequencing data derived from an HBV integrated human cell line(PLC/PRF/5) indicated that TSD could recover the full profile of HBV integration events, especially for the regions with the complex human-HBV genome integrations and multiple HBV rearrangements. Compared to other long read analysis tools, TSD showed a better performance for detecting complex genomic structural variants. TSD is publicly available at: https://github.com/menggf/tsd.
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