Transforming Sample Management at Biodesix

How Biodesix uses Sample Manager for their extensive biorepository

Contents: Background | Introduction | Challenges | Journey | Why LabKey | Results | Conclusion



Biodesix is a leading diagnostic solutions company specializing in lung disease diagnostics. They operate two clinical diagnostic laboratories in Colorado and Kansas, running the IQLung™ portfolio and the Nodify Lung® portfolio. Additionally, Biodesix partners with biopharma, diagnostic, and academic organizations to develop novel therapies. Over time, they’ve accumulated a substantial biorepository of over 150,000 samples and associated data, presenting numerous data management challenges.



Faced with managing an extensive biorepository, Biodesix embarked on a journey to transition from a manual method of sample inventory management to using LabKey’s robust sample management system: Sample Manager.



Biodesix faced several challenges with their sample management:

Manual Data Management: Their existing system relied on manual processes, leading to incomplete and scattered associated data.

Lack of Standardization: The data management system lacked standardized fields, making it difficult to accommodate all sample types.

Training and Turnover Issues: The absence of a well-defined system led to challenges during personnel changes, resulting in the loss of critical steps.

Scalability: With the repository rapidly growing, the need for a more scalable solution became apparent as resource demands grew.


The Journey:

The process of migrating to Sample Manager took several stages:

Data Compilation: First, they began by requesting all available data from department stakeholders and combined over 160 individual manifests into a single master file. New fields were added as needed to ensure comprehensive data collection. 

Physical Verification: A quality control check was performed on the freezers in both the Colorado and Kansas labs. Sample identifiers were verified and recorded, along with their precise locations within the freezers.

Discrepancy Resolution: Any discrepancies found during the verification process were resolved in real-time. Missing data for some samples were also collected from respective departments.

Migration to LabKey: The validated data was migrated to Sample Manager. A trial application was used to test and review all processes before going live in production.

Customization: To capture sample data and reflect the reality of the lab, they customized naming patterns, storage configurations and workflows within the system.

Feedback: Frequent communication with the LabKey team during onboarding helped Biodesix fully adopt and optimize their use of the application.


Why LabKey:

There were four big reasons for choosing LabKey’s Sample Manager:

Audit Trails: The application offered easily accessible and readable audit trails, simplifying traceability of sample activity and movement.

Data Security: Cloud hosting, database encryption, and daily data backups were included, essential for maintaining data security.

Scalability: The application accommodated their large sample volume and the diversity of sample types received through biopharma partnerships without data limitations.

User-Friendly Interface: The intuitive design and user-friendly interface made it easy for all team members to navigate the system and access the data they needed.



Biodesix successfully migrated to Sample Manager and has since seen several improvements:

Traceability and Lineage: The system’s lineage management has improved project tracking and sample traceability, ensuring samples are tied to their source project.

Streamlined Communication: The workflow editor role in Sample Manager’s lab workflow management has enhanced communication between the biorepository and the laboratory by managing sample processing and requests.

Picklists and Jobs: The previous paper-based request system has been replaced by workflow jobs and picklists, granting the lab greater access to data for selecting the samples they need.

De-Identification: Sample Manager’s unique system-generated sample IDs have streamlined the de-identification process, making samples available for various internal projects.



Biodesix’s transition to Sample Manager has transformed their sample management processes, enhancing data integrity, traceability, and communication between the biorepository and the laboratory.


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