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LabKey and ORIEN Informatics at City of Hope

Presented By: Vincent La, City of Hope

Presentation Abstract: The Oncology Research Information Exchange Network (ORIEN) is a consortium of 18 institutions across the nation that brings together clinical and genomic data to further precision-based therapies. All patients are under a common protocol known as Total Cancer Care. Patients enrolled in this protocol are followed throughout their life allowing respective member sites to collect both clinical and genomic data. Specimens obtained from patients undergo whole exome sequencing and whole transcriptome sequencing at a qualifying vendor. City of Hope, the third institution to join the consortium, has recently moved forward with ORIEN and has begun sending specimens for sequencing with corresponding clinical data. As such, the institution has developed an ORIEN Informatics roadmap to support the data acquisition, governance, access, and downstream analytics. The roadmap supports Laboratory Information Management System (LIMS) data for specimen collection, clinical data stored in City of Hope’s enterprise data warehouse (EDW), and genomic data that will be accessible through the cloud as well as within City of Hope’s HPCC environment. Since the data of interest exists in disparate sources, a software solution was chosen in our roadmap for integration across systems. LabKey Server, an open source platform, is that solution. LabKey provides a graphical user interface, querying capabilities, and report building tools. The platform seamlessly integrates with the EDW, provides analytics of meta-data, supports API development, allows for collaboration, coordinates workflows, maintains an audit trail in a compliant environment, and acts as a user-friendly front door to many systems. LabKey will support the overarching goal of the ORIEN informatics roadmap to provide clinicians and researchers with data and tools to progress precision medicine.

Speaker Bio: Vincent La has been leading the informatics component of ORIEN (Oncological Research Information Exchange Network), a Precision Medicine research initiative at City of Hope Cancer Research Hospital in Duarte, California. He is the team’s project and data lead, bringing his experience in product management and data expertise from health startups and other health enterprises like Kaiser Permanente to the role. With the genomics from the ORIEN study, he works in the space of Radiogenomics where he collaborates with radiologists, data scientists, and the Precision Imaging Lab in discovering biomarkers for brain cancers and success or failures of CAR-T cell immunotherapies. Vincent has considerable experience in R programming and SQL, which he has used for quality control, data processing, and reporting for research at City of Hope. He received his Bachelor’s in Public Health: Infectious Diseases from UC Berkeley. Vincent has a desire to make an impact in Precision Medicine.

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