Data Management & Traceabity to Enable Validation, and Regulatory Compliance

The Connecticut-based Mount Sinai Genetic Testing Laboratory is CLIA-certified and provides dedicated sequencing services to both the Mount Sinai Health System in New York City as well as external clients. It took the Mount Sinai team just 18 months to build out a facility capable of running 50,000 clinical samples a year. In order to track data and maintain complete traceability as required for compliance, and to support sequencing at scale, the Mount Sinai team selected the Core LIMS as its laboratory information and workflow management platform. In just over a year, the system was deployed, and the lab was ready for the validation and auditing.

The lab sequences both clinical and research samples, most notably to support the Resilience Project, which is studying why some people remain healthy even when their DNA contains markers for specific illnesses. The lab runs a Mount Sinai-developed “SuperPanel” that tests for more than 700 genes contained in 4.4 MB of DNA covered by 25,000 amplicons.

What Does a LIMS Project Look Like for Sequencing at Scale?

Conducting large-scale sequencing required the lab to invest in automation and integration to move samples rapidly through the workflow—and that’s where Core Informatics comes in. We worked alongside the lab since before it acquired most of its instrumentation and personnel. As Todd Arnold, Ph.D., Managing Director of the Mount Sinai Genetic Testing Laboratory described in his webinar, How Mount Sinai Uses LIMS to Support Clinical & Research Genomics Workflows, the Core LIMS touches every step in the lab’s sample management and sequencing workflow, from the initial receipt of samples through sequencing, analysis, and aggregation of data for reporting.

Arnold’s team had aggressive goals. Two months after they engaged Core, the lab was accessioning its first samples, and LIMS configurations had been established to support this initial work. As samples moved through the workflow, the lab could determine in real-time what data the LIMS should track. Core’s Customer Success team working closely with members of the Mount Sinai LIMS team took the findings and used the data to tailor the LIMS to the lab’s needs. Two months after the lab went live, 6,000 samples had already been run through the system. Mount Sinai validated its LIMS implementation in preparation for the CLIA inspectors just a few months after the system was up and running, and the full audit occurred a few weeks later.

Arnold has praised the “level of discipline Core brought to the development process. They asked a lot of questions about how the system should look or how specific tasks related to the overall goals.” He characterized the questions from our team as resembling an interrogation, but also noted that this is exactly what is needed to develop a system that collects the right information to provide full traceability across every part of the workflow.