Case Studies

Storage and analysis of very large human genomic datasets for cancer research – UNSW

Dr Jason Wong from the Lowy Cancer Research Centre at UNSW, studies mutations in the non-coding portion of the genomes of cancer sufferers to provide a better understanding of cancer biology, new ways to personalise therapy for patients and open the door to potential novel cancer drug treatments.

Needing to transfer, store and perform intensive computations on a very large amount (650 TB) of controlled access human genome data from The Cancer Genome Atlas in the USA, members of our team worked closely with Dr Wong to deliver an integrated solution, with med.data.edu.au providing active storage of the genome data with robust access control, linked to high performance computing (HPC) facilities, to underpin the data analysis pipeline.

Storing and sharing large bio-imaging datasets across the globe – ANZAC Research Institute

Researchers led by Prof Hong Zhou and Prof Markus J. Siebel from the Bone Biology Unit at the ANZAC Research Institute study the effects of steroid hormones and growth factors on skeletal health in the context of ageing, arthritis, chronic stress and metastatic cancer.

Utilising x-ray microtomography (micro-CT) imaging to evaluate bone architecture and density is key when assessing bone health. X-ray data collected from genetically modified rodents, which lack glucocorticoid signalling in bone or cartilage cells has led to significant advances in the understanding of steroid hormone action in the skeleton.

Each dataset from the micro-CT instrument amounts to 2.5GB, with the study generating several TB per year. The large datasets are routinely efficiently uploaded to med.data.edu.au data storage at very fast speed using technology underpinned by Aspera FASP, and from there easily shared with various collaborators across Australia, Europe and North America.

Underpinning spatial query, analysis and display of health datasets – UNSW City Futures Research Centre

Prof Chris Pettit of the City Futures Research Centre at UNSW undertakes urban research from a spatial perspective, which allows for the integration of many data types (e.g. infrastructure, demographics etc.) across various level of geography which can be used to support an evidenced based approach to scenario planning.

In this demonstration project, med.data.edu.au is helping Prof Pettit to undertake spatial research on health-related datasets by securely hosting 3 health datasets that contain text-based address information: The National Health Services Directory (NHSD); NSW Fall-related injury hospitalisations and the MyHospitals dataset which includes address information of over 1,000 Australian public and private hospitals.

med.data.edu.au is also providing cloud-based tools to geocode this data, aggregate it into different levels of ABS geography resolutions (e.g. SA1 and SA2). This processed data is then made available through a machine to machine connection to the AURIN Portal (pictured). The portal comprises a sophisticated suite of spatial data query and analysis tools and allows these health datasets to be analysed with other comparable data available. AURIN provides access to over 1,200 other spatial datasets, and access to these additional datasets through med.data.edu.au provide an important contribution of data for the Australian urban research community to use to undertake research excellence and support city policy and decision making.

Read more at AURIN

Data for studying age-related bone loss and the biomechanics and micro-structure of bone – University of Melbourne

The Melbourne Femur Collection is a unique archive of human femoral bone tissue gathered (over the last 20 years) from around 600 individuals who died suddenly and unexpectedly without any major predisposing medical conditions or long periods of immobilisation. The collection also includes post-mortem clinical CT scans, micro-CT image data, and digitised microradiographs of thin sections of the bones.

The initial justification for the collection was for age-at-death determinations in a forensic context but as those responsible have collected more and more material they have come to realise that huge variations in patterns of bone tissue ageing are observed amongst persons of the same chronological age. While age-at-death determination from histomorphometry was not achieved, the serendipitous nature of science has meant that the greatest potential value for the collection is now being realised by studies of age-related bone loss (which may lead to osteoporotic fracture of the hip) and the biomechanics and micro-structure of bone.

med.data.edu.au is providing the DaRIS/Mediaflux bio-medical imaging data management platform operated by VicNode which holds 1,931 objects comprised of 2.23TB of imaging data. DaRIS enables the data custodian of the collection to easily browse and search data. Requests for subsets of data, once approved, can easily be created and shared with external researchers.