Automation, Efficiency and an End-to-End Solution:

How Semaphore Extended BaseSpace Clarity LIMS to Lay the Groundwork for Scale.


About Helix

Helix is a personal genomics company with a mission to empower every person to improve their life through DNA. One of the largest clinical exome sequencing labs in the world in the world, the Helix laboratory is responsible for the processing, analysis and secure storage of their customer’s DNA data.

Helix sets itself apart by using Next Generation Sequencing (NGS) and a proprietary assay that includes a medical exome as well as a microarray backbone to power research, clinical products, and nonclinical applications. Helix partners with health systems and research institutions to maximize the impact of the genome and to encourage disease prevention in communities.

Executive Summary

As one of the world’s fastest growing personal genomics companies, Helix required the structure and flexibility of a customized Laboratory Information Management System (LIMS) to handle an exponential increase in their daily sample throughput. As a large scale CLIA certified and CAP accredited laboratory, there existed no margin for error at any stage, whether it be sample intake, analysis, or data storage.

Semaphore Solutions worked with Helix to automate and extend BaseSpace Clarity LIMS without impacting lab throughput. The end result was a highly automated Clarity LIMS which ultimately allowed for a significantly increased volume of data.

Challenges Semaphore Addressed

In order to achieve their growth goals, Helix needed the following components to ensure their infrastructure could handle an influx of data:

  • A stable implementation of the extended BaseSpace Clarity LIMS that ensured upgrades could undergo testing and versioning without disruption of the current process.

  • A highly automated LIMS which reduced human interaction with the samples, reduced human error, and increased overall lab efficiency.

  • A LIMS that ensured the lab maintained its CLIA- and CAP- accreditation by supporting validation and quality control while providing a seamless integration between Helix’s business systems, instrument integrations, wet lab, and the overall lab processes.

The Semaphore Solution
  • Custom Workflows: Custom LIMS workflows were designed to automate lab processes and form the basis of the integration with Helix instrumentation. Custom solutions were integrated at each stage in the wet lab workflow, spanning from extraction to sequencing. 
  • Automation: As part of the automation process, Semaphore developed a series of messaging systems between the BaseSpace suite and other internal tools that allowed for lab technicians to interact with the automated processes. This allowed the lab technicians to requeue samples, cancel process etc. with very little manual work or interference with the LIMS.   
  • No Impact on Throughput: Semaphore took care to implement a solution that wouldn’t impact Helix’s high volume lab. It was imperative that the extended Clarity LIMS implementation and upgrade followed a strict procedure that ensured validation by providing testing and staging processes and allowed for continuous improvement. 
  • Collaboration: Throughout implementation, Helix and Semaphore worked collaboratively. This ensured that Helix was always in control of the code base and was able to review and ensure that any developments would adhere to the strict CLIA- and CAP-accreditation guidelines. 
  • Internal Training: Helix is an evolving and dynamic company, which will continue to develop new features and products. As such, Semaphore trained Helix’s internal software team to maintain and update their solution into the future. Semaphore will continue to collaborate with Helix’s team whenever they are called upon. 

Helix required a custom solution in order to maximize lab and data efficiency. It was essential that this solution to be implemented without impacting lab throughput. The implementation of the extended Clarity LIMS, lab automation and software support provided by Semaphore Solutions provided the necessary infrastructure for the launch of the first online consumer marketplace for DNA-Powered products. 

Semaphore’s custom workflows allow Helix’s lab to serve a growing customer base and easily process an increasing daily sample volume. Helix’s partners know that they can rely on customer data being analyzed, stored and accessed in a timely fashion by multiple third party apps and integrations. As a result, Helix was able to easily scale up their production for the launch of their marketplace and grow into a company with over 150 employees.  

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