Custom LIMS Solution

An integrated LIMS for a Large Scale Molecular & Genomic Pathology Hospital Laboratory

Top 15 Hospital

About the Laboratory

This large scale Molecular and Genomic Laboratory is part of a hospital system that is ranked within the top 15 in the United States, and as such is responsible for the analysis of a high volume of clinically significant samples. This highly complex, state of the art laboratory runs many different types of analyses and is staffed with a large, multidisciplinary team.

Executive Summary

Genomic laboratories have complex workflows. From accessioning through to analysis, the number of possible interactions between sample, staff, and instrument can be overwhelming. Many labs purchase Laboratory Information Management System (LIMS) software planning to streamline, regulate, and document workflows. LIMS systems in these environments are sometimes employed directly out of the box with great success, but often require extra configuration to best support the specific needs of complex genomic laboratories.

Semaphore Solutions understands that when it comes to LIMS, one size does not fit all. As an Illumina Partner, Semaphore specializes in BaseSpace Clarity LIMS implementation, configuration, and support. With years of experience in Clarity configuration, Semaphore’s development team is expert at building laboratory solutions. Our team members are also experts at integrating LIMS with Electronic Medical Record systems (EMR’s) via HL7.

A major US hospital molecular diagnostic laboratory found their needs exceeded out of the box LIMS capabilities. Semaphore Solutions has worked with laboratory stakeholders to design and deliver significant customizations to BaseSpace Clarity LIMS. Semaphore continues to work with the lab, expanding and evolving LIMS in this complex and dynamic environment.

Challenges Semaphore Addressed

Like many other complex genomic laboratories, this lab found that tasks such as repetitive paperwork, data entry, and by-hand calculations took time away from lab technicians doing their actual job: analyzing clinical samples.

They needed a LIMS that aligned with their workflow while eliminating redundancy and streamlining process. They also required a LIMS that could be fully integrated into their existing EMR and LIS. Semaphore worked closely with the lab management staff to help them meet all of these requirements. Through teamwork and an open, iterative process, Semaphore has provided a custom solution that spans the entire laboratory workflow: 

The Semaphore Solution

Accessioning: Semaphore’s team is highly proficient in HL7, and integrated LIMS with pre-existing Laboratory Information Systems (LIS’s) and Electronic Medical Record systems (EMR’s). The integration with the pre-existing LIS enables Accessioning staff to continue working with the software they already know and trust, but with the advanced functionality of BaseSpace Clarity LIMS.

Sample Processing: All extraction protocols are batched to increase efficiency and reduce lag time. A barcode is generated for each sample to allow for easy re-extraction at a later date.

Analysis Preparation: Semaphore’s customizations automate plate assignments, reagent calculations, and dissolution tables. The automation of repetitive tasks reduces the potential for human error while saving time and money.

Benchtop Support: Bench notes are automatically generated and displayed on tablets to ensure placement tables, calculations, notes, and reminders are kept handy at each workstation. Comprehensive, easily accessible bench notes enable lab technicians to remain focused on the task at hand.

Instrument integration: Bi-directional instrument integration enables lab staff to skip data entry and get straight to work. Output automatically feeds back into the LIMS, enabling quick turnaround between testing and delivering results.

Internal Reports: An internal tracking report is generated for each sample, simplifying retroactive reporting of analytic factors. Tracking reports are especially useful for audits and accreditation.


This Large Scale Molecular & Genomic Pathology laboratory required a customized, fully integrated LIMS to track and manage complex daily workflow. Semaphore’s dedicated development team were able to meet their needs by creating custom solutions across all stages of the laboratory workflow.


  • A reduction in repetitive tasks enabled lab technicians to focus more on sample analysis and less on paperwork.

  • Batched protocols increased efficiency and reduced test turnaround time (TAT).

  • Internal tracking mechanisms allowed for transparency into all lab processes, ensuring consistency and quality.

  • Integration with pre-existing EMR and LIS simplified accessioning and enabled ordering physicians to action results sooner.

Technologies: PCR, NanoDrop, Mass Spec, HL7, Assays

Laboratory System Integration
We integrate laboratory information management systems (LIMS), laboratory information systems (LIS), order and results systems, requisition provisioning, Enterprise Resource Planning (ERP), Customer Relationship Management (CRM), project management and custom portals. No matter your workflow, we make it happen.

Analysis Pipeline Integration
We support your analysis solution. Our software professionals provide efficient solutions for ensuring sequencing data securely enters your analysis platform of choice, and final reports are delivered to the right place.

Instrument Integration
Automating the exchange of setup information and result data with instruments increases laboratory efficiency and accuracy. We have experience integrating the full range of molecular diagnostic instruments, from QC instruments to sequencers to automated liquid handlers.

Electronic Medical Record (EMR) Systems Integration
EMR integration ensures that critical test and patient information enters the laboratory efficiently and error-free, and results are communicated accurately and quickly. Whether using EPIC, Cerner or another EMR system, we can integrate your laboratory systems via HL7.

Laboratory Scalability
Increasing sample throughput requires significant automation of laboratory processes and information management. Our team builds and maintains some of the highest throughput NGS labs in the world and can apply that experience to help you achieve your throughput goals.

Order Management
In addition to tracking physical samples, clinical diagnostic laboratories need to efficiently manage the orders that accompany samples. From the physician portal to the dashboard that manages order status, our customized system ensures that your lab’s orders are processed efficiently and accurately.

Business Solutions
We build custom solutions that support business process related to the laboratory workflow including Order and Result Portals, HIPAA Compliant Databases, Panel Selection Websites, Project Management Dashboards. If you can’t find off-the-shelf solutions, talk to us about how we efficiently build solutions that exactly match your requirements.

Software Engineering Services
We understand that laboratory software needs change over time. Let us support your team with a single developer or full team.

“Semaphore provides software expertise for Helix’s Clarity LIMS implementation. They have provided excellent project management, technical leadership, and quality software development that was crucial to the successful launch of our high volume lab. It’s refreshing to collaborate with an attentive team during complex implementations.”

Tony Le, Product Manager