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LIMS Customization Key to High-throughput Whole Genome Sequencing
Contact usIllumina 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.
Scaling Clarity LIMS to support population-scale genomics required sophisticated workflow logic, system validation, and coordination across multiple teams and technologies.
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.
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.
The scale and complexity of the 100,000 Genomes Project introduced challenges far beyond a typical LIMS implementation. Genomics England, Illumina, and Semaphore Solutions needed to integrate new sequencing technology, automation protocols, and regulatory standards within a single high-performance LIMS platform.
A primary challenge was incorporating Illumina’s NovaSeq platform into the existing Clarity LIMS infrastructure. The NovaSeq introduced multiple new library preparation and analysis pipelines, which had to coexist with established HiSeq workflows. This required complex, conditional workflow logic to support multiple entry points, subprocesses, and branching decision paths, all while maintaining clean sample traceability and user experience.
In addition, the project required significant automation—especially integrating Hamilton liquid handlers into the LIMS-controlled workflow. Semaphore developed new protocols and automation scripts to minimize manual steps, maximize throughput, and ensure consistency across batches.
Validation was another critical dimension. Operating in a clinical genomics environment, the system had to meet rigorous data integrity and traceability requirements. Semaphore delivered a validated production system with meticulous configuration control, version management, and testing. This required close collaboration with Illumina’s R&D and lab services teams as well as the customer’s own clinical informatics and compliance personnel.
Beyond the initial implementation, Semaphore was responsible for continued system enhancements, workflow evolution, and release support—all without disrupting sequencing operations. This required a highly structured and responsive support model, focused on stability, adaptability, and performance at scale.
The collaboration between Illumina Lab Services (ILS) and Semaphore Solutions exemplifies a strategic partnership that effectively addresses the complexities of scaling genomic sequencing operations. A critical aspect of this collaboration was the seamless integration of the NovaSeq sequencing platform into ILS’s existing Laboratory Information Management System (LIMS). This integration required meticulous customization to accommodate multiple library preparations and analysis pipelines, ensuring that the new workflows coexisted harmoniously with the pre-existing HiSeq workflows.
Semaphore’s approach was rooted in a deep understanding of high-throughput Next-Generation Sequencing (NGS) workflows. By developing advanced workflow logic and implementing new protocols for Hamilton automated liquid handlers, they managed the increased complexity introduced by the NovaSeq platform. This not only streamlined laboratory processes but also enhanced automation, reducing the potential for human error.
A significant challenge was deploying a new, validated LIMS solution with minimal disruption to ongoing operations. Semaphore’s commitment to rigorous testing and quality assurance ensured that all software releases met the high standards required for clinical laboratory accreditation. Their collaborative and agile methodology allowed for flexibility as project requirements evolved, resulting in a LIMS implementation that was precisely tailored to ILS’s operational needs.
In the realm of genomic medicine, the ability to efficiently scale sequencing operations is pivotal for advancing research and delivering timely clinical insights. The successful partnership between ILS and Semaphore Solutions underscores the importance of integrating cutting-edge technology with existing laboratory infrastructures to achieve high-throughput sequencing capabilities.
By customizing and extending the Clarity LIMS, Semaphore facilitated the seamless incorporation of the NovaSeq platform, thereby enhancing ILS’s capacity to process a diverse array of genomic data. This integration not only bolstered operational efficiency but also ensured that data management processes remained robust and compliant with clinical standards.
The achievement of sequencing 100,000 genomes by December 2018 stands as a testament to the efficacy of this collaboration. It highlights how strategic partnerships and tailored informatics solutions are essential for laboratories aiming to operate at population-scale genomics. Such advancements are crucial for accelerating the translation of genomic data into actionable medical interventions, ultimately contributing to improved patient outcomes and the advancement of personalized medicine.
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