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Leveraging technology to maximise the value of human biospecimens
Dr Miranda Smith
The Peter Doherty Institute for Infection and Immunity
Human biospecimens are a highly valuable resource for researchers – but they are expensive to collect and store, and specimen banking is often fragmented and siloed.
A biobank is an organised collection of biological samples for research use, and usually includes a selection of clinical or health data. These samples might include blood, saliva, skin, or tumours, and they are very expensive to maintain.
Biobanks tend to vary in how they are organised, their level of organisation, and their sophistication. Some in Australia are highly organised but for infectious diseases they are mostly small, study-specific, and unlinked.
The Australian Partnership for Preparedness Research on Infectious Disease Emergencies (APPRISE) Centre for Research Excellence (CRE) recognised the importance of establishing an infectious diseases biobank to help inform emergency responses prior to COVID-19, but progress towards a single national biobank of existing specimens was stymied by issues of governance and data ownership.
The COVID-19 pandemic provided the perfect real life case study demonstrating the value of timely access to existing specimens and creating a sense of urgency to develop a solution. BioGrid was able to address some of the previous barriers by offering a technical solution that removed the need to create a new, single biobank. Instead, the BioGrid platform leveraged six existing COVID-related biobanks nationally, linking them under their current governance arrangements but enabling their specimens to become more widely searchable.
APPRISE provided the collaborations and infectious disease expertise for the virtual biobank, and BioGrid developed the technical architecture.
The advantage of the BioGrid solution includes that the collection and distribution arrangements for individual collections have not changed, but researchers can easily use a single website to get an overview of samples available from multiple collections. Data held by individual collections does not “move” or get transferred to a central database; instead, data aggregation for the portal is done whilst maintaining the individual governance and access arrangements associated with each biospecimen collection.
This approach is far more efficient than trying to harmonise disparate collections, and BioGrid’s overarching governance structure and technical platform makes it easier to deal with different jurisdictions and locations, public and private organisations, and varying technical architecture.
A ‘minimum information’ model has been developed that ensures the essential information needed to create a harmonised view is available for the virtual portal. This model defines the information required from each collection for searching via the virtual biobank portal. The aggregate data viewed from an online search request is held in temporary memory while the end user is querying the virtual biobank databases and is destroyed once the session ends.
Providing a portal to existing collections also means that when access is required, it can happen quickly. The individual collections are updated in real time without impacting any of the BioGrid infrastructure, and the search results include all current data.
At all times, custodians of the specimen collections have full control over who can access their specimens, and BioGrid’s unique operating model means no specimen data is ever stored anywhere other than in the original collection database.
When access to a collection is granted, BioGrid’s platform documents data elements and integrates them into a common platform.
BioGrid’s involvement has been essential as they are experienced in handling health data and have provided support to get the necessary ethical approvals and technical solutions in place. We couldn’t have done it without them.
Phase one of the APPRISE Virtual Biobank provides relatively high-level information about specimen collections to researchers using the portal.
In the future, there are plans to integrate more collections and provide more detailed information on participating collections. This would include integrating details about ethical approval and access processes into the BioGrid portal to improve the usefulness of the search results for researchers.
Dr Miranda Smith is an Academic Specialist providing project and strategic support to the APPRISE Executive across the research areas and cross-cutting themes. She co-ordinates APPRISE activities and facilitates stakeholder engagement.
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