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

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MARC

Börjesson, VanjaGothenburg University,Göteborgs universitet,Core Facilities, Bioinformatics,Core Facilities, Bioinformatics (author)

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

Article/chapterEnglish2022

Publisher, publication year, extent ...

2022-02-20
Springer Science and Business Media LLC,2022

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LIBRIS-ID:oai:gup.ub.gu.se/314040
https://gup.ub.gu.se/publication/314040URI
https://doi.org/10.1186/s12864-022-08376-0DOI
http://kipublications.ki.se/Default.aspx?queryparsed=id:148926535URI

Supplementary language notes

Language:English

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SwePubSwePub

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Subject category:ref swepub-contenttype
Subject category:art swepub-publicationtype

Notes

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.

Subject headings and genre

NATURVETENSKAP Biologi Genetik hsv//swe
NATURAL SCIENCES Biological Sciences Genetics hsv//eng
Next-generation sequencing
Transgenic insertion site
PPM1D
Chimeric
reads
Discordant read pairs
Transgenic organisms
integration sites
animals
Biotechnology & Applied Microbiology
Genetics & Heredity

Added entries (persons, corporate bodies, meetings, titles ...)

Martinez-Monleon, AngelaGothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Department of Laboratory Medicine(Swepub:gu)xmaang (author)
Fransson, Susanne,1975Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Department of Laboratory Medicine(Swepub:gu)xfrans (author)
Kogner, P.Karolinska Institutet (author)
Johnsen, J. I.Karolinska Institutet (author)
Milosevic, J. (author)
Davila Lopez, MarcelaGothenburg University,Göteborgs universitet,Core Facilities, Bioinformatics,Core Facilities, Bioinformatics(Swepub:gu)xdavma (author)
Göteborgs universitetCore Facilities, Bioinformatics (creator_code:org_t)

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In:Bmc Genomics: Springer Science and Business Media LLC23:11471-2164

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Genetics

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By the university: University of Gothenburg; Karolinska Institutet

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