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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 .
      (© 2022. The Author(s).)
    • References:
      Exp Anim. 2020 Aug 5;69(3):279-286. (PMID: 32051389)
      Sci Rep. 2017 Jan 25;7:41120. (PMID: 28120936)
      Methods Mol Biol. 2013;1064:315-36. (PMID: 23996268)
      Reprod Domest Anim. 2005 Aug;40(4):269-81. (PMID: 16008757)
      PLoS One. 2012;7(11):e50348. (PMID: 23185606)
      Nat Biotechnol. 2011 Jan;29(1):24-6. (PMID: 21221095)
      Methods Enzymol. 1992;216:415-26. (PMID: 1479912)
      J Biotechnol. 2002 Sep 25;98(2-3):145-60. (PMID: 12141984)
      J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712)
      Genome Biol. 2018 Nov 19;19(1):199. (PMID: 30454069)
      BMC Genomics. 2014 May 14;15:367. (PMID: 24884803)
      Brain Struct Funct. 2010 Mar;214(2-3):91-109. (PMID: 19937345)
      Nucleic Acids Res. 2017 May 5;45(8):e62. (PMID: 28053125)
      Cancers (Basel). 2021 Oct 31;13(21):. (PMID: 34771656)
      Bioinformatics. 2014 Oct;30(19):2811-2. (PMID: 24930139)
      PLoS One. 2014 May 14;9(5):e96650. (PMID: 24827921)
      Sci Rep. 2013 Oct 03;3:2839. (PMID: 24088728)
      Nat Biotechnol. 2017 Apr 11;35(4):316-319. (PMID: 28398311)
      Genom Data. 2015 Sep 08;6:175-81. (PMID: 26697366)
      Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
      Biotechniques. 2006 Dec;41(6):715-9. (PMID: 17191616)
      Plant Biotechnol J. 2003 May;1(3):155-65. (PMID: 17156029)
      Rev Sci Tech. 2005 Apr;24(1):285-98. (PMID: 16110896)
    • 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
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