TransgeneR: a one-stop tool for transgene integration and rearrangement discovery using sequencing data

Meng, Guofeng

doi:10.1101/462267

Cited by 4 publications

(5 citation statements)

References 16 publications

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“…Similarly, Abrams et al (2014) uses chimeric reads to identify the insertion site, while the discordant read pairs are used to identify structural variants with third party tools. Lastly, transgeneR [ 12 ] is an R package that applies a two-round alignment, it relies on split reads and coverage to identify the TIS and calculates the confidence of the call.…”

Section: Resultsmentioning

confidence: 99%

“…We scrutinized the intermediate files and despite considering that the correct chimeric reads were recovered, no candidates were suggested after the calculation of the window score. Regarding transgeneR [ 12 ], the installation was not properly tested given that only the results of the test dataset were provided within the documentation. While running the package, some errors were encountered preventing the analysis to properly finalize, thus no TIS were reported.…”

Section: Resultsmentioning

confidence: 99%

“…With the advent of sequencing data, today it is more cost effective to identify the transgene insertion site (TIS) with in-silico routine analysis. There have been several efforts to predict TIS using next generation sequencing (NGS) data that rely on chimeric reads and discordant read pairs [ 8 – 12 ], i.e. pairs that map in non-canonical ways.…”

Section: Introductionmentioning

confidence: 99%

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TC-hunter: identification of the insertion site of a transgenic gene within the host genome

et al. 2022

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Background Transgenic animal models are crucial for the study of gene function and disease, and are widely utilized in basic biological research, agriculture and pharma industries. Since the current methods for generating transgenic animals result in the random integration of the transgene under study, the phenotype may be compromised due to disruption of known genes or regulatory regions. Unfortunately, most of the tools that predict transgene insertion sites from high-throughput data are not publicly available or not properly maintained. Results We implemented TC-hunter, Transgene-Construct hunter, an open tool that identifies transgene insertion sites and provides simple reports and visualization aids. It relies on common tools used in the analysis of high-throughput data and makes use of chimeric reads and discordant read pairs to identify and support the transgenic insertion site. To demonstrate its applicability, we applied TC-hunter to four transgenic mice samples harboring the human PPM1D gene, a model used in the study of malignant tumor development. We identified the transgenic insertion site in each sample and experimentally validated them with Touchdown-polymerase chain reaction followed by Sanger sequencing. Conclusions TC-hunter is an accessible bioinformatics tool that can automatically identify transgene insertion sites from DNA sequencing data with high sensitivity (98%) and precision (92.45%). TC-hunter is a valuable tool that can aid in evaluating any potential phenotypic complications due to the random integration of the transgene and can be accessed at https://github.com/bcfgothenburg/SSF.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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TC-hunter: identification of the insertion site of a transgenic gene within the host genome

et al. 2022

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“…Some of these SVs contribute to the phenotype diversity and susceptibility to diseases (Brandler et al 2016;Truty et al 2018), which draws more attention in disease studies. Complex SVs can also be observed in the genome with genetics instability (Weischenfeldt et al 2013;Lupski 2015), virus integration or transgenic modification (Zhao et al 2016a;Meng 2018), which may generate complex rearrangement of external DNA sequences and random integration in the host genome.…”

Section: Introductionmentioning

confidence: 99%

TSD: A computational tool to study the complex structural variants using PacBio targeted sequencing data

Meng¹,

Tan²,

Fan³

et al. 2018

Preprint

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The PacBio sequencing is a powerful approach to study the 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 internal or external sequences. However, there is still no tool designed to uncover their structural organization in the host genome. 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 KEYWORDS structural variants long reads genomic structure PacBio 1 INVESTIGATIONS

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“…Some of these SVs contribute to the phenotype diversity and susceptibility to diseases (Brandler et al 2016; Truty et al 2018), which draws more attention in disease studies. Complex SVs can also be observed in the genome with genetics instability (Weischenfeldt et al 2013; Lupski 2015), virus integration or transgenic modification (Zhao et al 2016a; Meng 2018), which may generate complex rearrangement of exogenous DNA sequences and random integration in the host genome.…”

mentioning

confidence: 99%

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

Meng¹,

Tan²,

Fan³

et al. 2019

G3 Genes|Genomes|Genetics

Self Cite

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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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TransgeneR: a one-stop tool for transgene integration and rearrangement discovery using sequencing data

Cited by 4 publications

References 16 publications

TC-hunter: identification of the insertion site of a transgenic gene within the host genome

TC-hunter: identification of the insertion site of a transgenic gene within the host genome

TSD: A computational tool to study the complex structural variants using PacBio targeted sequencing data

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

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