BioGrid: providing solutions for your research data challenges 

Infection-related mortality is the leading cause of early death for many adult Australians with blood cancers undergoing leukemia treatment or allogeneic haematopoietic stem cell transplantation. Until now, systematic surveillance of these infections in clinical settings took too long and required too many resources to be feasible.

Researchers at the Peter MacCallum Cancer Centre are tackling this issue using a next-generation digital platform called EINSTEIN (Enhancing Infection Surveillance to Transform Excellence In National cancer care), a tool for providing clinicians with a platform for understanding and flagging infections. EINSTEIN draws on a digital learning health framework and data science to detect serious and emerging infections in the immune compromised cancer population.

BioGrid provides the data sharing and linkage infrastructure and services underpinning the initiative, as well as establishing the data agreements and streamlining data governance between participating institutions with the BioGrid collaboration agreement. BioGrid also securely codes patient data, ensuring that no identifying information is provided to researchers who have approval to use the data.

Data issue:

• Accessing curated hospital pathology data on paediatric and adult patients to validate automated surveillance system
• Collating data from multiple sources into an automated, integrated digital health surveillance platform for the detection of infections in immune compromised patients

BioGrid solution:

• Streamlined governance process for ethical approval to access hospital data
• Curation of hospital EMR data extractions to validate and refine NLP algorithms for detection of infections
• Provision of national data sharing and linkage infrastructure
• Secure coding of patient data, ensuring no identifying information is provided to authorised researchers

The National Cancer Cohort Platform (NCCP) project is the first collaboration of its kind, incorporating KConFab, Australian Ovarian Cancer Study, Variants in Practice (ViP) Study, Lifepool, and Melanoma Research Victoria cancer cohort studies as well as BioGrid Australia, the Department of Health Services Research at Peter MacCallum Cancer Centre and the Victorian Comprehensive Cancer Centre (VCCC) Alliance.

The cohorts hold a rich range of valuable data relating to melanoma, ovarian, breast and prostate cancers amassed over many years. Collectively they have an estimated 96,000 participants and hold around 127,000 biospecimens, 1 million mammograms, and 120,000 detailed pedigrees.

BioGrid has a major role in the project providing software development of the new portal and the re-development of two ageing cohort databases. In addition, BioGrid is assisting with the multi-institutional agreements needed for cohort studies to on-board and join the platform, which ensures consistent data security and privacy standards.

Data issue:

• Bringing together five influential national cancer cohort studies into a single virtual searchable platform, including linkages to biospecimen repositories and familial pedigrees
• Integration of data from ageing databases into modern platform

BioGrid’s solution:

• Establishment of data sharing agreements and streamlining of data governance with participating cohorts leveraging the BioGrid Australia Collaboration Agreement
• Development of ‘data commons’ as a standardised approach for participant and sample tracking data capture that will facilitate cohort management for existing and future cohorts
• Re-development of two ageing cohort databases to ensure longevity of historic and future data collection
• Development of a portal to accommodate the needs of cohort data managers, researchers, clinicians, participants and consumers
• Provision of national data sharing and linkage infrastructure
• Secure coding of patient data to protect patient and clinician privacy

The ADDN project commenced in 2012 as a joint initiative between the Australia and New Zealand Society for Paediatric Endocrinology and Diabetes (ANZSPED) and Juvenile Diabetes Research Foundation (JDRF) Australia. The overall aim of the ADDN project was to facilitate research and improve the health of people with diabetes.

The first phase of ADDN established a secure and centralised data repository hosted by the University of Melbourne, holding de-identified longitudinal demographic and clinical data for more than 5,000 children and adolescents with Type 1 diabetes.

In 2016 the Australian Diabetes Society (ADS) joined ANZSPED and JDRF Australia for the second phase of ADDN which expanded the number of paediatric centres and extended recruitment to include adult centres. With this, ADDN increased its data capture to provide richer and more complete information about the natural history, clinical progression and most effective treatment regimens for all people living with Type 1 diabetes.

Data issue

• Linking diabetes patients across paediatric and adult hospitals to understand patient journey of care
• Linking National Diabetes Services Scheme (NDSS) Continuous Glucose Monitoring (CGM) registrant data to clinical data for CGM program evaluation

BioGrid solution

• Leverage the BioGrid Australia Collaboration Agreement to streamline data governance arrangements with participating sites to enable BioGrid to receive patient identifying information for record matching purposes
• Within secure environment, generation of unique patient record linkage key per patient to enable:
  • Paediatric and adult data to be linked within the ADDN registry
  • NDSS CGM data to be linked to ADDN registry clinical data to enable NDSS CGM program evaluation analyses

The National Antibiotic Allergy Network (NAAN) has developed a framework for collaborative health services research in antibiotic allergy and part of this action is the formation of a database auditing inpatient antibiotic allergy testing, known as the International Network of Antibiotic Allergy Nations (iNAAN) study.

This database provides a platform for informing a standardised assessment and oral challenge procedure and a method for capturing the resulting data, which can then be used for auditing and improving hospital procedures and national policy.

The database is complemented by a smartphone app (NAAN App) that clinicians can use to guide their decision-making. The data collected by the app is not stored locally but is safely transferred via the cloud to a REDCap database securely hosted by BioGrid.

BioGrid provides secure data storage and handling, along with existing ethics approval for our data sharing platform.

Data issue

• Hosting and data integration of mobile app and iNAAN databases for hospital bedside penicillin allergy assessments

BioGrid solution

• Secure hosting and maintenance of mobile app and REDCap database for national and international use
• Ingestion via API of mobile app data to REDCap database
• Benchmark reporting from linked data created for participating sites

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.

Data issue

• Visibility of siloed biosample collections to understand what and where biosamples of research interest are held to improve efficiency 

BioGrid solution

• Build secure federated web-based portal to enable visibility of biosamples available across multiple biosample collections
• Retain existing biosample collection ethics and governance
• Query approved limited biosample information via APIs between APPRISE portal and the biosample collection sites where the type of query is stored, but not the data queried enabling a virtual search solution that met existing biosample collection ethics and governance