Bioimaging Bank: Linking Medical Imaging and Biobanking Data for Cancer Research Daniel Moses BSc(Hons) MBBS Hons MEngSc PhD FRANZCR DABR Medical Director Research Imaging NSW Level 1 Building 3, Prince of Wales Hospital. https://research.unsw.edu.au/research-imaging-nsw Professor, Graduate School of Biomedical Engineering, UNSW
The Project in a Nutshell EXISTING DATABASES: POWH and UNSW HSA Biobank project: ● standardised universal consent process, collecting and linking both clinical and biological data to specimens ● dedicated biobanking database contains biological information related to the tumours from approximately 5000 patients treated at POWH. ● specimens are stored, managed and distributed from the UNSW Biorepository Medical image data: ● stored in a large RIS/PACS in the Medical Imaging Department of Prince of Wales ● includes all radiology and nuclear medicine studies since 2008 AIM: Linking clinical imaging data to the established biobanking database facilitating much easier examination of both biological and imaging data in specific cohorts of interest and allowing: ● improved imaging feature extraction from medical images for predicting biological properties of tumours ● combining medical image and biological features of tumours into a prognostic model ● improved personalised treatment OUTPUTS: ● Extend the pathway for extracting medical imaging data to other partners in the South Eastern Sydney Local Health District ● Promote and support research by linking medical imaging data and biological tissue data for cancer patients through a single comprehensive database ● Bioimaging bank would be available to any researcher in Australia with a suitable research project and with ethics approval on application
Key Issues Ethics Extraction and Matching of Existing Patients from Biobank Database ● csv file Participant_PPID Participant_MRN Site Participant_MRN Site - 2 Participant_Registration Date Participant_MRN Participant_MRN - 2 Participant_Gender Participant_MRN Site ID - 1 Participant_MRN Site ID - 3 Participant_Date Of Birth Participant_MRN Site - 1 Participant_MRN Site - 3 Participant_Consent Date Participant_MRN - 1 Participant_MRN - 3 Participant_MRN Site ID Participant_MRN Site ID - 2 Participant_Consent Comments Radiology Information System (RIS) ● installed in 2008 (Centricity RIS-i 4.2 Plus) and runs on Windows Server 2003 and an Oracle database ● contains all of the patient report and examination data performed in the SESLHD (including Prince of Wales Hospital) ● since 2008 and includes 3.4 million recorded procedures Importation of Medical Imaging Reports into the Biobank Database ● OpenSpecimen 6.1 with an Oracle database ● more fields need to be created within the database for each patient ● attempt to import the large number of medical imaging reports into the current kept crashing the system
Lessons Learnt Ethics Coordinating Between Large Institutions Dealing with a Diverse Operational Team Communication and Collaborations with Key IT Staff Outside of the Project Patient Privacy and Data Security ● Transfer of data ● RIS managers in the Medical Imaging Department at POWH allowed password access to a database Dealing with Outdated and Fragile Software/Computer Systems ● RIS: used a “view” of database - functioned as a protective mechanism → only allowed us to query a confined portion of the database without using too many database resources ● Biobank: support team advised an upgrade to a mySQL database which works better with the OpenSpecimen & is more stable Custom Writing Software ● Python programming language ○ cx_oracle python library to connect to and query the database (https://oracle.github.io/python-cx_Oracle/) ○ python csv library to read & write csv files (https://docs.python.org/3/library/csv.html) ● patients to query are listed in the csv file supplied by Biobank ● each time query is run it will generate all reports for one patient ○ script loops through each patient, querying the database and recording the result ○ recorded in a local database that the query has been performed on that patient on such-and-such a date ○ built-in time delay to avoid spamming the server
Acknowledgements Dr Laughlin Dawes (Radiologist and Computer Scientist at POWH) Dr Jitendra Jonnagaddala (Data Scientist, UNSW Medicine) Dr Anusha Hettiaratchi , (Manager, UNSW Biorepository, Mark Wainwright Analytical Centre[MWAC]) Dr Carl Power (Head, Biological Resources Imaging Laboratory in the MWAC) Dr Stephanie Macmillan (Operations Manager,TCRN) Professor David Goldstein (Director, TCRN, UNSW)
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