Case Study: Clinical Lab Achieves High-Throughput NGS Performance with a Configurable Lab Platform

Executive Summary

A leading clinical laboratory, processing vast numbers of samples daily for next-generation sequencing (NGS), requires extraordinary efficiency, productivity, and stringent quality control. This organization sought a comprehensive informatics platform to manage intricate sample volumes, complex instrumentation, and multi-faceted workflows. The Sapio Platform, a science-aware™ LIMS solution, provides out-of-the-box NGS templates, built-in collaboration, and robust sample management capabilities, enabling high-throughput performance, enhanced visibility, and streamlined operations for clinical NGS workflows.

The Customer: A Leading Clinical Laboratory

Company Overview

This is a leading clinical laboratory that processes up to tens of thousands of samples each day. It operates with massive volumes of data, fast turnaround times, and stringent quality control requirements. The lab requires extraordinary levels of efficiency and productivity to meet these demands.

Background

Clinical labs require an end-to-end solution that enables them to configure quickly, maintain complete visibility over their entire process, collaborate across multiple sites, and get results faster. This is especially true for next-generation sequencing (NGS), which brings unique demands for intricate sample management, continuous monitoring, instrument integration, and complex workflows involving steps like sample preparation, library preparation, and sequencing, each requiring proper reviews and approvals. Effectively tracking a multitude of NGS samples while rapidly generating results with high standards for quality and accuracy is all but impossible without a proper informatics platform.

The Challenge: Complexities in Clinical NGS Workflows

NGS workflows present significant challenges for clinical labs, demanding a robust informatics solution to manage high-throughput operations and ensure data integrity.

Specific challenges include:

Inefficient Results and Reporting: Generating comprehensive reports for management and patients is time-consuming without integrated data and automated, configurable reporting capabilities.
High Sample Volume and Velocity: Labs process thousands of samples daily with urgent turnaround times, requiring efficient and accurate input, tracking, and prioritization, which manual methods cannot sustain.
Disparate Instrumentation and Materials Management: A wide range of instruments generate varied data formats, complicating analysis. Continuous monitoring, validation, and tracking of instruments, materials, and reagents are complex, leading to disjointed data and errors without integration.
Intricate and Inflexible Workflows: NGS involves numerous interdependent steps requiring reviews and approvals. Many existing solutions lack the flexibility for labs to tailor workflows to their unique needs, forcing inefficient retrofitting or custom coding.

The Solution: The Sapio Platform for High-Throughput NGS

Why Sapio Sciences Was Chosen

The need for a comprehensive platform that provides built-in NGS templates and enables rapid development for specialized requirements led to the adoption of the Sapio Platform. As the world’s first truly science-aware™ lab informatics solution, the Sapio Platform enables leading clinical labs to maximize efficiency and productivity across their NGS workflows.

Implementation Overview

The Sapio NGS LIMS solution is built for NGS scientists to get up and running quickly. With out-of-the-box NGS templates built in from the start, clinical labs can begin to realize value immediately. The platform is purpose-built to address NGS’ intricate sample management requirements at scale.

Key Features

Sapio NGS LIMS Solution: Built specifically for NGS scientists to get up and running quickly.
Out-of-the-Box NGS Templates: Provides immediate value and rapid deployment for common NGS workflows.
Built-in Collaboration: Supports custom views by role, commenting on samples and plates, and visibility into previous updates.
Purpose-Built Sample Management: Addresses NGS’ intricate sample management requirements at scale.
- Barcode scanning for direct sample input into the NGS LIMS.
- Configurable views for sample status, number of extractions needed, and more.
- Ability to assign plate numbers directly within the LIMS.
- Notifications for improperly ordered samples.
Centralized Dashboard for Results Processing: Allows viewing how many confirmations each sample is awaiting.

Comprehensive Visibility: Provides comprehensive visibility over sample lineage.

The Results: Maximized Efficiency and Productivity in NGS Workflows

The Sapio Platform enables leading clinical labs to maximize efficiency and productivity across their NGS workflows by addressing their specific challenges.

Key outcomes and benefits provided by the Sapio Platform include:

Accelerated Onboarding and Streamlined Sample Management: The Sapio NGS LIMS solution allows NGS scientists to get up and running quickly, realizing immediate value through out-of-the-box NGS templates. It facilitates easy input and location of samples at each stage of the NGS workflow, enabling quick viewing of critical information and accounting for nuances. The platform supports massive sample volumes with agility and efficiency through features like barcode scanning, plate assignment within the LIMS, and notifications for improperly ordered samples, ensuring ongoing accuracy.

Enhanced Workflow Visibility, Collaboration, and Data Integrity: The platform offers built-in collaboration features, supporting custom views by role, commenting on samples and plates, and providing visibility into previous updates, fostering better team coordination. It delivers comprehensive visibility over sample lineage and a centralized dashboard for results processing, allowing users to view how many confirmations each sample is awaiting. By automating sample input via barcodes and providing notifications for improper orders, the platform reduces manual inaccuracy, and its ability to track sample status and lineage supports stringent quality control requirements.

Lessons for Clinical NGS Labs

This case study highlights critical considerations for clinical laboratories seeking to optimize their NGS workflows and achieve high-throughput performance:

Streamline Results and Reporting: Opt for platforms that provide integrated data and automated, configurable reporting capabilities, enabling the generation of meaningful reports with custom rules.
Prioritize a Comprehensive, Configurable Platform: Seek an end-to-end informatics solution that offers built-in templates for rapid deployment, alongside the flexibility and extensibility for specialized and evolving NGS requirements.
Address Sample Volume and Velocity with Automation: Implement systems that enable easy, automated input and tracking of samples (e.g., via barcodes) to manage high throughput, prioritize urgent samples, and maintain accuracy.
Ensure Integrated Instrument and Materials Management: Choose a platform that can integrate data from diverse instruments, facilitate continuous monitoring and validation, and track materials/reagents to avoid disjointed data and errors.
Support Multi-Faceted and Adaptable Workflows: Select solutions that allow tailoring to unique lab requirements, manage interdependent steps, and ensure proper reviews and approvals without relying on tedious custom coding.

Conclusion

This leading clinical laboratory has found a comprehensive answer to the demands of high-throughput NGS workflows in the Sapio Platform. By leveraging its science-aware™ NGS LIMS solution, the lab can effectively manage intricate sample volumes, integrate complex instrumentation, and streamline multi-faceted processes. The platform’s out-of-the-box templates, collaborative features, and robust sample management capabilities enable the lab to achieve extraordinary levels of efficiency and productivity, ensuring rapid, high-quality results in clinical diagnostics.

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FAQ

Q: What problem did the NGS clinical lab face?
A: Managing tens of thousands of NGS samples daily with complex instrumentation and manual workflows.

Q: How did the Sapio Platform address this?
A: It offered out-of-the-box NGS templates, barcode scanning, and centralized dashboards for efficient, high-throughput workflows.

Q: What specific capabilities did Sapio provide?
A: Role-based collaboration, custom sample views, and integration-ready APIs for instrument and plate tracking.

Q: What improvements were seen?
A: Accelerated onboarding, enhanced sample lineage tracking, and real-time workflow visibility.