case-study

Case Study: Baylor HGSC Optimizes High-Throughput Genomics with Sapio LIMS as Digital Backbone

Executive Summary

The Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC), a world leader in genomics, upgraded its homegrown LIMS to Sapio LIMS. This transition was driven by the need to manage the increasing growth and complexity of its sequencing processes. The Sapio LIMS, integrating core LIMS, materials, storage, instrument run monitoring, and post-sequencing analysis modules, has enabled precise tracking of expensive reagents, improved speed and accuracy of lab robots, facilitated advanced post-benchwork analysis, drastically reduced reliance on manual tracking methods, and expedited cross-training, solidifying its role as an integral part of HGSC’s future in high-volume, complex DNA sequencing.

The Customer: Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC)

Company Overview

The BCM-HGSC (Baylor College of Medicine-Human Genome Sequencing Center) is a world leader in genomics. It operates one of the most technologically advanced laboratories in the world, with the ability to process a large volume and variety of samples and protocols.

Background

Previously, a custom-built LIMS was the mainstay of the laboratory work at BCM-HGSC, tracking samples from intake to sequencing analysis. This system, while foundational, was insufficient when dealing with the increasing growth and complexity in their sequencing processes.

The Challenge: Overcoming Limitations of a Custom-Built LIMS

The previously created custom-built LIMS at BCM-HGSC had several shortcomings that needed to be addressed:

• It functioned mostly as a plain ledger to record very limited information from the laboratory bench work.
• It was a disparate set of applications strung together to track and record a few sample attributes.
• The data collected during the benchwork was not visible to the lab personnel unless exposed through a custom report.
• It did not capture any lab events apart from the benchwork information. Common events such as sample failure or reprocessing were tracked outside of the system using Microsoft Excel sheets, emails, and ad hoc meetings.
• It lacked an inventory management system and supported a very basic storage system.

The Solution: Sapio LIMS as the Digital Backbone

Why Sapio Sciences Was Chosen

The HGSC software team evaluated numerous industry-leading LIMS applications. Their criteria included the need for a system that was extensible, configurable, and customizable; had a strong track record and vision for future functionalities; and was battle-tested, highly available, and scalable. 

After an exhaustive evaluation process, the center concluded that the Sapio Sciences Informatics Platform met most of the objectives and requirements.

Implementation Overview

The HGSC team collaborated with the Sapio Sciences team in the initial phase of the development to understand the best practices, configuration details, and methodology for developing the highly customized workflows. The HGSC team then took over and added the proprietary and complex business logic for the center.

Key integration and deployment steps included:

• Robotics Integration: Manual robots were converted to work in a semi-autonomous mode and communicate directly with the LIMS using the REST API web services.
• Printer Integration: Legacy Zebra printers were integrated with the LIMS.
• Reporting System Integration: The Reports system gleaned data from the LIMS using the APIs provided by the Sapio LIMS.
• Instrument Interfacing: The instrument run monitor interfaced with various sequencers.
• Post-Sequencing Pipeline Integration: The post-sequencing pipeline interfaced with the LIMS using custom-built interfaces.

The HGSC adopted a staggered rollout strategy. The implementations for each protocol were phased in gradually, enabling the HGSC to immediately realize the benefits of Sapio.

Key Features

Sapio LIMS partnered with HGSC to support the HGSC lab pipeline. The implemented Sapio modules include:

• Sapio LIMS core
• Materials Management
• Storage Management
• Instrument Run Monitor
• Integrated Chat
• LIMS Robotic Software
• Post-Sequencing Analysis
• Reports and Data Visualization

The Results: Enhanced Efficiency, Visibility, and Scalability

Adoption of the Sapio Platform resulted in significant improvements across HGSC’s lab operations.

• The materials management module enabled precise tracking of expensive reagents and reduced wastage.
• The benchwork robots were programmed to communicate directly with the Sapio LIMS system, improving speed and accuracy.
• The copious amount of data collected during benchwork enabled the lab to perform post-benchwork analysis and identify issues in advance of the expensive sequencing process.
• Adoption of the Sapio Platform resulted in a drastic reduction in the volume and use of emails and Excel sheets, thereby improving communication between the lab groups.
• The consistent UI, look, and feel led to expedited cross-training of the lab personnel.
• The out-of-the-box ad hoc reporting enabled lab managers to query the data instead of requesting reports from the software team.

Rapid Response and Scalability (COVID-19 Example)

All these benefits stemming from a feature-rich and multipurpose LIMS were apparent during the COVID-19 pandemic. The HGSC was able to rapidly develop a highly flexible and functional protocol with Sapio LIMS, integrate with their robotics, and reporting systems, and deploy over a single weekend. The center has been one of the major testing centers in Texas. This was a good example of how the center could use Sapio LIMS to fulfill one of its core objectives: to serve the community.

Customer Quotes

“The Sapio software was a game-changer for our lab operations, streamlining our processes and reducing wastage.” – Harshavardhana Doddapaneni, Director of Research Laboratory, HGSC

“The Sapio LIMS platform has enabled us to record and track the complex lab processes in minute detail. The LIMS has truly been a force multiplier for our lab.” – Jianhong Hu, Director of Clinical Laboratory, HGSC

Lessons for Genomics Leaders

This case study offers critical insights for other world leaders in genomics and high-throughput laboratories:

• Move Beyond Legacy Systems for Scale: Custom-built or disparate systems can become limiting factors for growth and complexity, necessitating an upgrade to a modern, unified LIMS.
• Prioritize Extensibility, Configurability, and Scalability: A robust LIMS must be able to adapt to evolving needs, integrate seamlessly with existing infrastructure (e.g., authentication, robotics, instruments), and handle increasing volumes of data and samples.
• Demand Comprehensive Data Visibility and Event Tracking: Ensure the LIMS captures all lab events, not just benchwork, and makes data readily visible and queryable to all relevant personnel, reducing reliance on manual, external tracking methods.
• Seek Out-of-the-Box Advanced Functionality: Look for LIMS solutions that offer built-in features like inventory management, storage management, and ad hoc reporting to accelerate implementation and provide immediate value.
• Leverage APIs for Automation and Integration: Utilize the LIMS’s API capabilities to program robots for direct communication, integrate with sequencers and post-sequencing pipelines, and streamline data flow across the entire lab.
• Adopt a Staggered Rollout Strategy: Phased implementation of protocols can allow for immediate realization of benefits while managing the transition to a new system effectively, including training and bug resolution.

• Choose a Feature-Rich, Multi-Purpose Platform: A comprehensive LIMS can act as a “force multiplier” for lab operations, providing flexibility and rapid deployment capabilities to respond to unforeseen demands, such as pandemics.

Next Steps

The Human Genome Sequencing Center at Baylor College of Medicine is experiencing dramatic growth in the volume and complexity of DNA sequencing, and the Sapio LIMS is an integral and essential part of its future.

Conclusion

The Baylor College of Medicine Human Genome Sequencing Center successfully upgraded its digital backbone by adopting Sapio LIMS, moving beyond the limitations of its homegrown system. This transition has enabled precise tracking of reagents, improved robotic efficiency, facilitated advanced data analysis, streamlined communication, and expedited cross-training. Demonstrating its critical value during the COVID-19 pandemic, the Sapio LIMS has proven to be a flexible, feature-rich, and essential platform, positioning HGSC to manage its dramatic growth in DNA sequencing volume and complexity while continuing to serve its community.

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FAQ

Q: What challenge did Baylor HGSC face with their legacy LIMS?
A: Limited data visibility, reliance on external tracking tools, and lack of integrated inventory and instrument management.

Q: Why was Sapio LIMS chosen?
A: For its extensibility, scalability, and ability to support complex sequencing and automation workflows.

Q: How did Sapio improve lab operations?
A: Enabled direct robotic integration, post-benchwork analysis, automated reporting, and better reagent tracking.

Q: What’s the long-term impact?
A: Baylor can now support high-volume genomic processing with streamlined training and rapid protocol deployment.