Bioinformatics platform helps manage biospecimen library

Wednesday, 02 October, 2019 | Supplied by: AXT Pty Ltd


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The Auckland Region Tissue Bank (ARTB) is a critical component in New Zealand’s medical research infrastructure. As a central facility for storing blood and tissue samples, the tissue bank has a library that could hold the secrets to unlocking cures for existing and future chronic diseases and illnesses. These samples could be made available to researchers from the University of Auckland as well as throughout New Zealand and to collaborators further afield.

Having a collection of samples for medical research is highly desirable, as it acts as a repository that researchers can access at any time. The ARTB currently houses around 125,000 samples, with the number having grown exponentially in the last four years. Without a facility like ARTB, collecting samples would be a tedious and onerous task that uses a lot of researcher time and slows medical research. However, having the samples is just one part of the equation. Being able to access the right samples with specific clinical parameters to isolate specific strains, genetic traits or tissue types is of equal importance.

“When the University of Auckland created the ARTB and acquired the existing library of samples from Middlemore Hospital Tissue Bank, there was a need to unify the bioinformatics system and we were looking for a robust and structured system able to manage our biobank in a constructive way,” said Phillip Shepherd, Regional Tissue Bank Manager. “We chose OpenSpecimen as the system was able to be customised to our specific needs and the developers, Krishagni, were dedicated to biobanking and had a vast depth of experience that we could tap into.”

Originally developed by Krishagni Solutions with funding from the National Cancer Institute (NCI) in the US to aggregate and manage biospecimen data, OpenSpecimen has continued to evolve into a comprehensive open-source bioinformatics platform. It is now used in over 65 biobanks around the world.

ARTB engaged with Krishagni right from the start of its journey. By being involved in ARTB’s workflows and practices, Krishagni was more easily able to advise and customise OpenSpecimen to the tissue bank’s requirements.

“The open source nature of OpenSpecimen allows us to make changes to the system by ourselves and not be locked into using the developer for every change that we need,” Shepherd said. “Of course there are modifications that we get Krishagni involved with, and they are always very accommodating and responsive.”

Alice Rykers, the ARTB’s OpenSpecimen super user and Tissue Bank Technician, said, “I really enjoy using it and have been thoroughly impressed with how it works. It gives us excellent visibility and the query module is a Godsend with its ability to quickly generate reports and display data.”

While the ARTB’s collection of tissue samples is strategically focused on medical research areas such as blood cancers, cardiac, breast, sarcoma, melanoma and endometriosis, the organisation is always open to collaborating with other research groups where it can offer a service. This will no doubt see its valuable library continue to grow, increasing the relevance of ARTB — all with the knowledge that OpenSpecimen will be able to grow with it.

Image caption: The Auckland Region Tissue Bank biospecimen storage facility.

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