100,000 Genomes and Beyond

LIMS Customization Key to High-throughput Whole Genome Sequencing

Illumina Lab Services

About the Laboratory

Illumina Lab Services (ILS), based in Cambridge, U.K., has developed a set of informatics tools to enable the delivery of genomic clinical and research services at population scale. Semaphore was an early collaborator with ILS on their Laboratory Information Management System (LIMS), customizing and extending Clarity LIMS to create a highly automated system.

By December 2018, ILS reached the milestone of 100,000 genomes sequenced, demonstrating their capability for high-throughput whole human genome sequencing at scale. This LIMS now supports a range of workflows on HiSeqX and NovaSeq sequencing platforms for cancer and rare genetic disease patients.


ILS’s workflows include multiple library preparations, sequencing platforms, and analysis pipelines. The introduction of the NovaSeq sequencing platform significantly increased the complexity of LIMS workflow management.

Key goals:

  • Integration between LIMS, NovaSeq, and BaseSpace Sequence Hub to automate the flow of sequencer data into the analysis pipeline for interpretation.

  • Integration of NovaSeq workflows while maintaining the operation of existing HiSeq X workflows.

  • Development of improved workflow logic and new Hamilton automated liquid handler protocols to manage the complexity associated with the new NovaSeq workflows in the highly automated laboratory.

  • Installation of a new, validated, LIMS solution with minimal disruption to the existing production system, enabling successful accreditation for this clinical lab.

The Semaphore Solution

Quick Ramp-up: Semaphore Solutions’ long-standing relationship with Illumina as a software development partner ensured a quick ramp-up of the Semaphore software team.

Collaborative Approach: The Semaphore team worked with the CRO laboratory team using a collaborative, agile process. As the implementation progressed and requirements evolved, this flexible approach ensured the final implementation is an excellent fit with the laboratory’s final processes.

Scaling Throughput: The Semaphore team’s expert knowledge of high-throughput NGS workflows ensured that the ILS LIMS is built for scale.

Validation: Semaphore’s commitment to quality supported ILS’s high standards for laboratory quality control and demanding accreditation process. All software releases were rigorously tested by the Semaphore team prior to validation by the ILS team.

Bioinformatics: Semaphore’s expertise in bioinformatics system integration ensured sequencer output is efficiently managed and processed by the BaseSpace Sequence Hub analysis platform for diagnostic interpretation and reporting.

Expert Training: Semaphore trained the ILS team to use and maintain the LIMS implementation. As an Illumina partner, Semaphore will continue to support the LIMS into the future.


As ILS builds on the successful sequencing of 100,000 genomes, the addition of the NovaSeq platform expands sequencing options as the lab aims to increase efficiency and throughput. Semaphore’s high standards for software development ensured that the LIMS was prepared for final validation and accreditation by the ILS team. With a commitment to continuous improvement, ILS and Semaphore will leverage knowledge gained from this implementation to improve laboratory processes and efficiency into the future.

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.