Sapio LIMS Case Study: Baylor College of Medicine

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

Previously, a custom-built LIMS was the mainstay of the laboratory work and it tracked samples right from intake to sequencing analysis.

The Sapio LIMS software could be a game-changer for our lab operations, streamlining our process and reducing wastage.
– Harshavardhana Doddapaneni, Director of Research Laboratory, HGSC

Why the HGSC Struggled With Its Previous LIMS

Although the center's homegrown custom-built LIMS was simple, flexible, and easy to maintain, it had several shortcomings:

It functioned mostly as a plain ledger that recorded very limited information from the laboratory benchwork.
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 like sample failure, reprocess, etc. were tracked outside of the system using Excel sheets, emails, and ad hoc meetings.
It lacked an inventory management system and supported a very basic storage system.

A Quest for Solutions

The HGSC software team embarked on a quest for the best LIMS software on the market and evaluated some of the industry leading LIMS available.

The objectives were simple. The HGSC needed a LIMS that:

Was extensible, configurable, and customizable.
Had a good reputation and a vision for future functionality.
Was battle tested, highly available, and scalable.
Had mature implementation of cross-cutting concerns-such as security, auditing, logging-to comply with the various regulation standards.
Delivered out-of-the-box functionality for advanced LIMS features, like inventory management, storage management, and ad hoc reporting.
Had the ability to seamlessly integrate with the center's authentication mechanism.

After an exhaustive evaluation process, the center concluded that Sapio LIMS met most of its main requirements.

Does your lab currently operate on a custom-built or generic LIMS system?
Contact us to discuss your lab management software needs.

Solution at a Glance

Together, the HGSC and Sapio Sciences custom built a lab pipeline to suit the center's various needs. The modules in this custom product included:

Sapio LIMS core
Instrument Monitor
Material Management
LIMS Robotic Software
Storage Management
Post Sequencing Analysis
Instrument Run Monitor
Reports and Data Visualization

Implementation

The HGSC team collaborated with the Sapio Sciences team in the initial phase of development to understand the best practices, configuration details, and methodology for creating the highly customized workflows.

The HGSC team then took over and added its proprietary and complex business logic. The manual robots were converted to work in semi-autonomous mode and communicate directly with the LIMS using the REST web services.

Sapio LIMS Solution Highlights

Zebra Legacy printers were integrated.
The Reports system gleaned data from the LIMS using the APIs provided by the LIMS.
The Sapio LIMS Run Monitor interfaced with the various sequencers.
Post Sequencing pipeline interfaced with the LIMS using custom-built interfaces.

diagram of HGSC Sapio solution
HGSC Sapio Implementation

The HGSC adopted a staggered rollout strategy and the implementations for each protocol was phased in gradually, but the team immediately realized the benefits of the new Sapio LIMS product. For instance:

Precise Tracking - The Material Management module enabled the precise tracking of expensive reagents, which avoided wastage.
Speed & Accuracy - The benchwork robots communicated directly with the LIMS, which improved speed and accuracy.
Post-Benchwork Analysis - The copious amount of data collected during benchwork allowed the lab to perform post-benchwork analysis and identify issues before the expensive sequencing process.
Improved Communication - The drastic reduction in the volume and use of emails and Excel sheets improved communication between the lab groups.
Cross Training - The consistent UI and user-friendly platform expedited cross training of lab personnel.
Data Queries - The out-of-the-box ad hoc reporting enabled lab managers to query data on their own instead of requesting reports from the software team.

What Our Clients Thought About Their Customized Solution

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

Since Sapio LIMS Adoption

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

Is your organization looking for a better lab management solution?
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