Since most of the tools that predict transgene insertion sites from high-throughput data are not publicly available or not properly maintained, Bioinformatics Core Facility developed an open source tool, said Marcela Davila, manager at Bioinformatics Core Facility.
“When researchers approached us with their research problem, we developed this solution and took the opportunity to provide an automated service for the scientific community as a whole."
Recently a paper was published in BMC Genomics journal.
Used in the Study of Malignant Tumour
To demonstrate the TC-hunter applicability, it was applied to four transgenic mice samples harboring the human PPM1D gene, a model used in the study of malignant tumour development. The team identified the transgenic insertion site in each sample and experimentally validated them with Touchdown-polymerase chain reaction followed by Sanger sequencing.
Transgenic animal models are crucial for the study of gene function and disease, and are widely utilized in many areas. The random integration of a transgene may alter crucial genes or regulatory regions.
TC-hunter 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.
International collaboration - Funded by SSF
The tool is developed in collaboration with
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden.
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, USA
The project is funded by Swedish Foundation for Strategic Research, SSF.
