Rare diseases are broad in phenotypic traits and far reaching in impact. Today, approximately 7,000 different rare diseases affect an estimated 350 million individuals worldwide.¹ Difficulty in the understanding, diagnosis, and treatment of rare diseases stems from a lack of available data about any one disease at any one research site. The volume of data needed to produce authoritative discovery about any one rare disease requires the collaborative pooling of phenotypic, genotypic, and clinical information from many disparate sources.
LabKey is helping research networks advance understanding about rare diseases by providing a flexible data management platform to help overcome key data integration challenges including:
Integrating Data from Multiple Clinical Sites
Researchers and clinicians need access to a substantial pool of data in order to identify disease trends and determine appropriate treatment for patients. In the case of rare disease where the occurrence of a disease within the population is not commonly seen, integration of data from multiple clinical sites is essential to identifying a patient’s course of treatment.
LabKey Server facilitates the collection and integration of rare disease data from multiple clinical sites by providing:
- Operational data portals for data collection and preparation at clinical sites.
- Data processing pipelines for transferring data to an integrated repository.
- De-identification of personally identifiable information in clinical datasets.
Achieving Consistent Data Structures for Disease Data
In order for data to be integrated in a meaningful way, data generated at each clinical site must follow a consistent data structure. When data is structured correctly, researchers can query across data sources identify patterns in disease.
LabKey Server provides tools to help teams structure rare disease research data correctly during collection, and QA features to combat human error including:
- Data entry forms for clinical data collection tied to underlying data structures.
- Spreadsheet templates for offline data collection and bulk upload to LabKey data structures.
- Quality control features like lookups, aliases, and validators identify and correct errors found in data prior to integration with other sources.
Providing Access to Integrated Data
Integrating data collected from patients of rare disease helps clinicians make data-driven treatment decisions and research teams understand the genesis of the disease and the potential pathways to its cure. The data access needs of these different interest groups often vary, and the ability to control access to data at a granular level is essential to maintaining patient privacy without hindering research progress.
LabKey Server provides tools to control access to rare disease data and ensure appropriate use including:
- Role and group-based permissions for managing access to projects and folders.
- The ability to flag and remove PHI fields from data sets for collaborators without PHI-level permissions.
- An audit log that captures all access of and actions taken against a dataset.
Genomics England and LabKey: Creating and Securing “A Dialogue Between the Clinical Context and Researchers”
Genomics England has been working with LabKey to develop a LabKey Server-based data management and exploration portal that would facilitate the knowledge sharing dialogue between clinicians and researchers as part of the UK’s 100,000 Genomes Project. The initial phase of this collaboration centered around providing clinicians and researchers access to centralized phenotypic and sample information gathered from rare disease patients and their families at sites across the UK while ensuring security and privacy of patient information.