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Identifying Pseudogenes in the Human Genome – New Tool Developed Together with Sahlgrenska University Hospital

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A new, practical bioinformatics tool (PΨFinder) has been developed for the identification and visualization of processed pseudogenes (PΨgs). These genes are present all across the human genome, but little is known about their function and impact. Being able to identify them and their location, will give key information on different disease conditions, and improve diagnostics.

The project was funded by The Swedish Foundation for Strategic Research, SSF, and the team behind the tool consists of experts from Bioinformatics Core Facility together with researchers from the Institute of Biomedicine as well as Sahlgrenska University Hospital

“This collaboration has been crucial in developing the tool and making it useful for clinical work. When Anna Rohlin and her team first reached out to us with their samples to confirm if what they had found was actually pseudogenes, we created this tool and found that it can be useful in general to scan other types of samples too, said Marcela Dávila, manager at Bioinformatics Core Facility. 

Example of visualized data from the PΨFinder tool
Example of visualized data from the PΨFinder tool

User friendly interpretation of the results

PΨFinder tool can automatically identify novel PΨgs from DNA sequencing data and determine their location in the genome with high sensitivity (95.92%). It generates high quality figures and tables that facilitate the interpretation of the results and can guide the experimental validation. 

The tool helps us to "filter out" the pseudogens from samples so that we can experimentally validate them and try to interpret their meaning.It can also complement analysis and evaluation of genomics finding in inherited cancer and other genetic diseases,” said Anna Rohlin, Clinical Laboratory Geneticist at Sahlgrenska University Hospital 

Read the paper on PΨFinder published in BMC Bioinformatics 

Funding from SSF 

One of the goals of SSF is to contribute to the creation of research instruments, methods, and techniques as well as skills for research infrastructure. Core facilities, being an open-access research infrastructure, is therefor a natural part of the project. The tool is available under the GPLv3 license.

All researchers can contact our facility for support, but the tool itself is also open access and can be downloaded from our GitHub page, which also hosts other SSF projects, Marcela said.