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

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
    • Abstract:
      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 .
      (© 2022. The Author(s).)
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    • Grant Information:
      RIF14-0081 Stiftelsen för Strategisk Forskning; PR2018-099 Barncancerfonden; NCp2015-0061 Barncancerfonden
    • Contributed Indexing:
      Keywords: Chimeric reads; Discordant read pairs; Next-generation sequencing; PPM1D; Transgenic insertion site; Transgenic organisms
    • Publication Date:
      Date Created: 20220221 Date Completed: 20220222 Latest Revision: 20220224
    • Publication Date:
      20220224
    • Accession Number:
      PMC8859905
    • Accession Number:
      10.1186/s12864-022-08376-0
    • Accession Number:
      35184734