Extensibility

The Garvan Institute builds a genome factory and uses the BaseSpace Clarity LIMS API to automate processes and integrate with other systems

"The Clarity API is the very best part because we’re able to control every single aspect along the way."

Warren Kaplan, Chief of Informatics

The newest sequencing instruments, such as the Illumina HiSeq X Series, can sequence approximately 150 human whole genomes every three days, such that labs can build veritable genome factories. With this type of unprecedented throughput, how do you scale without sacrificing quality?

Ask Warren Kaplan, Chief of Informatics at the Kinghorn Centre for Clinical Genomics. When he set about to build one of the very first genome factories based on a fleet of Illumina HiSeq X instruments, he knew his IT infrastructure would need to scale and extend with other in-lab systems. He also knew that any unresolved systemic errors –with the instruments, workflows, data entry, etc.–would be amplified with such a dramatic increase in throughput. To address both of these issues, Kaplan relied on automation.

Using the BaseSpace Clarity LIMS application programming interface (API), Kaplan and his team integrated BaseSpace Clarity LIMS with other in-lab systems to initiate processes, eliminate the need for human interaction, and automate many of the steps in their workflow. That BaseSpace Clarity LIMS integrates with the HiSeq X instruments also enabled Kaplan and his lab to easily access run data from the instruments, monitor them, and pinpoint issues early on. As a result, his lab was able to scale to the increased throughput and maintain the same high quality by reducing the potential for error.

A LIMS should do much more than simply record laboratory procedures. BaseSpace Clarity LIMS is a development platform that enables you to extend the system to integrate with other in-lab systems, to automate or customize as necessary. Below are a few examples of how our customers have used our platform to streamline their organizations:

Access to the BaseSpace Clarity LIMS Application Programming Interface (API) provides your team with a complete developer resource that includes detailed documentation, video training, cookbook examples, and customer shared scripts to get you up-to-speed quickly.

About Warren Kaplan

Warren Kaplan is Chief of Informatics at the Kinghorn Centre for Clinical Genomics at the Garvan Institute. In this role, Kaplan empowers clinicians and researchers with practical tools and solutions to advance their science. Most recently, he has built a genome factory — to sequence a high volume of samples using Illumina’s HiSeq X Series instruments.

Dr. Warren Kaplan from the Garvan Institute discusses their new HiSeq X Ten powered genome factory

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