University of Newcastle and Hunter Medical Research Institute researchers just changed the game for future cancer research.
Together they have created “The Virtual Biobank” – a world first platform hosting 3D copies of human cancer tissues. With tissue samples digitised, it means everything is accessible for researchers whenever they need it, wherever they are.
“It currently takes many months before researchers are able to obtain tissue samples from a physical biobank and carry out investigations with it,” Chief investigators Dr Jamie Flynn, Dr Antony Martin and Dr William Palmer explain.
Not only that, but once a researcher has performed their study, that sample usually can’t be used again.
The Virtual Biobank changes all of this.
“Each digital cancer sample in The Virtual Biobank is made up of high resolution microscopy images in both 2D and 3D, plus important clinical and molecular information that provides the foundation for virtual research into cancer,” Drs Flynn and Palmer told us.
“We’ve taken a tiny sample from tumor biopsies stored at the Hunter Cancer Biobank and converted them into a virtual copy – enabling anyone around the world with an internet connection to carry out research from their computers or easily request access to the physical sample they need.”
Drs Flynn and Palmer say this process means the physical sample remains intact, but a 3D, digital copy with clinical and experimental information is kept online for future use.
“This is particularly critical for rare cancers, which are hard to study due to a limited number of samples.”
The first 20 breast cancer samples have already been uploaded to The Virtual Biobank, along with clinical descriptions.
The addition of 3D images was made possible by the innovative 3D Tissue Clearing and Lightsheet Microscope Facility (established by the same team in 2016) based at HMRI, which specialises in making tissue samples “see through” for cutting edge 3D microscopy.
Hunter Cancer Biobank Scientific Advisor, Dr Rick Thorne, said The Virtual Biobank is key to unlocking the third dimension of cancer tissues.
“Putting these samples in their true context for the first time will help researchers with many different problems, including how to get treatments to all of the cancer cells in tumors,” Dr Thorne says. “The project has kicked off with breast cancer, but the processes used by the team are applicable to any cancer tissue. It is remarkable this will happen online and we look forward to future expansions of the dataset.”
The University of Newcastle’s IT department and Library Research Services worked with the team to embed specialised software tools into the online platform – tolls that would otherwise be too expensive for researchers to access.
“We really wanted to make The Virtual Biobank interactive and dynamic, so with lead developer, Dr Bill Pascoe, and the Academic Research Computing Support team (ARCS), we developed a software toolkit for other people to contribute additional information such as findings from their own investigations,” Dr Martin said.
The “Tissue Tracker” section of the site lets researchers automatically log the experimental procedures for all new tissue samples coming into a lab – so no more hand-written notes – which means it is easier for other researchers to replicate experiments.
“Users can also create full 3D images for free by simply uploading their own microscopy data to our ‘Terastitcher Pipeline’, eliminating the need for expensive commercial software that can ordinarily cost upwards of $50,000,” Dr Martin pointed out.
While it’s still early days, the online platform holds promising future potential in areas of research, education – and even virtual reality.
Dr Palmer says people in the fields of engineering or computer science can now easily apply their knowledge to questions surrounding cancer, educators can access the site and use real-world examples to teach pathology to the next generation of cancer clinicians and researchers, and the team are also looking at converting the 3D data into virtual reality for education and general awareness.
“Hopefully soon, anyone with a smartphone and Google Cardboard could experience the internal environment of cancer tissue and bring about new insights,” Dr Palmer said.
Established through funding provided by the Australian National Data Service, The Virtual Biobank aims to work with biobanks around the country to continue uploading a variety of cancer tissues onto the platform. Donations to the project can be made via The Virtual Biobank website.
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