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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.
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.
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 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 X 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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