Computational Infrastructure Project Supports Translational Research Practice

The TCRN Translational Bioinformatics team has been awarded a UNSW Australia (University of New South Wales) Major Research Equipment and Infrastructure Grant for 2014, receiving funding to investigate the secure linkage of patient health information between a range of university and hospital databases.

The grant will be used to develop a broad computational strategy called Computational Infrastructure for Translational Research ("CITR"), designed to support translational cancer research projects across UNSW.

A data sharing project between Prince of Wales Hospital and UNSW was launched as the first stage of the CITR earlier this year. This project used health care standard HL7 messaging to make anonymised patient data in the hospital’s OmniLab and UNSW’s Aperio databases available to university researchers via UNSW’s caTissue system. In a first for the South Eastern Sydney Local Health District, and for UNSW itself, the process enabled researchers to combine pathology reports and whole slide images with information about biospecimens stored at the Lowy Biorepository.

“caTissue is an open source biospecimen management software tool that we use to store information on tissue samples collected for storage in the Lowy Biorepository,” says Jitendra Jonnagaddala, the TCRN’s Information Manager and the leader of the data integration project.

“While it is an excellent resource for collecting information about our biobank samples, it previously lacked the capacity to allow immediate and seamless transfer of patient health care data from hospital database systems.”

In order to receive HL7 messages from hospital data systems, the TCRN team were required to develop a process that was compliant with current patient privacy regulations.

“We worked with the UNSW IT department to build a secure server for clinical data hosting. This gave us a protected framework through which to transmit HL7 messages containing patient data from the OmniLab and Aperio systems,” Jonnagaddala says.

OmniLab is a hospital-based laboratory information system in which patient pathology reports and other health data is stored. The Aperio database is home to whole slide images of patient tissue samples, and is currently being used to store images of selected  samples in the Lowy Biorepository. Transmitting information from these databases to the caTissue system allows researchers viewing anonymised patient records to access that same patient’s pathology results and tissue slides in real-time. 

As well as reducing the timeframe for transmission of key patient data, the CITR project also minimises opportunities for human error, which were commonplace in the old system.

“Previously, researchers seeking pathology records from OmniLab had to manually enter the data contained in in scanned and hard-copy versions into caTissue, which often led to compromised data integrity as a result of typos and other man-made errors. The new process means that caTissue data fields are automatically populated when a pathology form is sent,” Jonnagaddala says.

Accessing Aperio’s whole slide images was another previously arduous process, with researchers having to request and transfer files of specific images onto their computers in order to view them. Now, the whole slide images appear as a link within the caTissue patient file; researchers need only click the link to view the file in real-time.

“What we wanted to do was create new pathways for information sharing that would give researchers faster, more secure access to patient data for the benefit of researchers, clinicians, and the patients themselves,” Jonnagaddala says.

“This project has resulted in a raft of positive outcomes for all the stakeholders involved, but I think patients, in particular, are really set to benefit. They can contribute to hospital-based research knowing their privacy is being absolutely protected.”

Future projects under the CITR banner will use the existing secure server to access real-time chemotherapy, pathology, clinical and associated experimental data from a range of hospital and research databases across New South Wales.