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City of Hope

Supporting Precision Medicine at City of Hope

LabKey Improves Data Accessibility for Total Cancer Care Protocol at City of Hope

Project Background

City of Hope is a comprehensive cancer care center gathering a wide range of clinical, genomic, and specimen data about patients undergoing treatment using the Total Cancer Care protocol. Working within the Oncology Research Information Exchange Network (ORIEN) consortium, the goal of this project is to bring together clinical and genomic data, making it available across the entire City of Hope enterprise where it can be used to improve precision-based therapies for future patients.

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.

Precision medicine involves aligning many complex elements, including deidentified patient data, whole genome or exome sequences, specific tumor sequences, specimen records from dozens of blood draws, biopsies, and more. 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. Many comparisons are made to improve health outcomes and expand knowledge: pathological to non-pathological tissue in a patient, samples between patients with the same health conditions, patients with pathologies to healthy patients. Insights can be drawn, treatments evaluated, and patient care made more certain and successful.


Gathering and integrating data from multiple locations can be difficult, particularly when protected patient data is involved and security is critical. The institution/enterprise needed to provide authorized users with access to diverse data from a wide variety of sources without resorting to piles of spreadsheets and manual alignment or home-built solutions. Researchers also needed to be able to generate visualizations and reports directly within the user interface to unlock trends and insights without leaving the combined data landscape.

Why Labkey

City of Hope determined that LabKey Server would integrate well with their existing data warehouse systems, provide users with graphical access to querying and reporting, as well as API access for developers and users performing more advanced analysis techniques. Additionally, LabKey Server is well suited to address the challenge of extracting historical information from a wealth of existing patient treatment records that were not originally stored in ways that align with other data.

More than just a software vendor, LabKey also supports City of Hope’s needs for team collaboration solutions, API development, and workflow integration, with an audit system that supports regulatory compliance. Looking ahead, LabKey solutions offer the expansion and flexibility required for scaling the City of Hope and ORIEN networks into broader use.

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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.
case study 2

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.


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.

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