Supporting Precision Medicine at City of Hope

Solution

There are two main components to how City of Hope is using LabKey Server:

1. Data aggregation from disparate sources and alignment with patient information
2. Management of the workflow process itself, including automated import and scripted transformation of data.

EPIC/Clarity holds current clinical data for the patients involved in both treatment and research. There is also a wealth of highly detailed information contained in paper charts, notes, and unstructured text from past treatment records for patients, collected without annotations that might have been helpful to future researchers. This rich data resource includes patient genetic histories, medical exams and diagnoses, sometimes long series’ of treatment records and test results, and outcome information. Extracting this information accurately into data for analysis is critical. LabKey Server can provide efficient tools for users to annotate and ensure the quality of the data.

Specimens obtained from patients are sent by City of Hope for both exome and transcriptome sequencing; this data is then linked with corresponding clinical data stored in EPIC and other various data sources. Aligning data by patient characteristics can unlock relationships between the individual and their disease progression, enabling future patients with these characteristics to receive more targeted treatment.

LabKey Server acts as the hub for integrating a multitude of data types, presenting it for further research and analysis. LabKey brings data together for holistic analysis of all the information available for a given patient or type of patient.

Genetic data is gathered from a mixture of medical exams, whole genome or exome sequences, specific tumor sequences, and pathology data. Researchers can isolate genetic markers and associate them with patient outcomes. Analyzing genes at levels of expression, the existence or expression of certain genes against measures of efficacy vs. toxicity and the prominence of side effects can all lead to better treatments, the development of more targeted drugs, and an improvement in prognosis for many patients.

For research purposes, City of hope also collects data through REDCap. The project data can be automatically synced with other patient data stored in LabKey. However, collecting and storing patient data is a difficult and complex problem. Unique protocols for obtaining consent across sites, disparate data structures and formats, and different underlying data storage systems must all be orchestrated together. LabKey Server offers data migration tools, a common set of analysis tools, including R reporting, and secure sharing that meets the needs of the City of Hope project for accessible and reproducible analysis.

Results

LabKey Server integrated all the necessary genomic, clinical, specimen, and workflow data, empowering users to easily join tables directly within the user interface without impacting colleagues who might have different needs. Researchers can customize as many individual views as they need and create personalized workflows that are not possible with other platforms.

LabKey takes care of the logistics and data validation, using automatic processes to extract, transform, and load the data, saving City of Hope time and removing human error.

Research teams can incorporate existing REDCap electronic data collection automatically, and focus on the science of precision medicine to improve patient treatments.

Future Work

The City of Hope began bringing data into the system in February 2018. Through publicizing early research results, the institutional ORIEN research project plans to expand usage within its City of Hope enterprise. Over time, this resource will grow and provide researchers with a wealth of information to use to understand the specific health story of the individual as a means to developing precision medicine.