Overcoming Bottlenecks in NGS Testing with an Effective LIMS

Clinical and molecular diagnostic testing is increasingly becoming more sophisticated, with technologies like next-generation sequencing (NGS) being used to detect genetic variation in patients with increased accuracy and lower costs. 

However, clinical labs specializing in NGS could be managing a 10–12 step process that runs from sample accessioning to test ordering to sample prep and sequencing to data collection, processing, and analysis to report generation and review. 

Any delay, at any step in the process, can have a significant impact on the processing of samples and reporting of results and may extend turnaround time (TAT), potentially delaying treatment for a patient. 

According to the U.S. Centers for Disease Control and Prevention (CDC), 70 percent of today’s medical decisions rely on lab test results. However, nearly 80 percent of labs report receiving complaints about their TAT. 

Consequently, it is necessary to identify and implement solutions to maintain the speed and accuracy of testing and reporting and improve TAT.

What key factors affect turnaround times?

TAT can be affected by a host of factors, but these issues can generally be boiled down to four key components: sample volumes, data complexity, lab resourcing, and preanalytical errors.

Sample volumes and workflow management

The average clinical lab processes thousands of samples a day, with larger commercial labs processing significantly more than the average. Dealing with this scale of samples requires effective process management, with even minor errors potentially leading to significant delays.

Data complexity

All samples will have unique challenges, but labs specializing in NGS are dealing with specific demands, including complex sample management, continuous monitoring, and instrument integration. Managing sample processing and deciphering the data generated requires extraordinary attention to detail, with the smallest disruption having a dramatic impact on overall TAT.

Lab resourcing

A shortage of skilled technicians, coupled with high workloads or staff burnout, can seriously affect the efficiency and accuracy of an NGS lab, leading to increased errors and extended TAT.

Preanalytical errors

Errors during the preanalytical phase can account for 60 percent to 70 percent of TAT delays in clinical labs. These issues, which often happen before the sample is even in the possession of the testing facility, include paper requisitions or disparate online ordering platforms, incorrect patient and specimen identification, delayed or faulty specimen collection, storage, transport, or accessioning.

Addressing the bottlenecks

The TAT of a lab can be affected at all phases, from initial sample acquisition to testing and reporting. Unclear ordering instructions at the start of the process can be compounded unless data, samples, and results are meticulously managed.

A modern, cloud-based lab information management system (LIMS) can help resolve the issues that result in poor TAT to improve the operational efficiency, accuracy, and reliability of the testing facility.

Deploying a modern LIMS across the entire testing workflow can significantly improve TAT, providing many key process improvements. 

For example, a clinician portal extends the testing workflow right into the doctor's office, allowing clinicians to create orders, track status, and receive results without the risk of losing data or missing information. By extending the testing workflow directly to relevant stakeholders, labs can improve communication, reduce frustration, and streamline the process from order placement to report delivery.

Digitizing the sample accessioning and order processing ensures a smooth and rapid transition from order placement to specimen processing and distribution to the appropriate internal workflows. Additionally, methods of identifying samples, such as barcodes and QR codes, remove the errors that could arise from registering samples manually.

Using a modern platform, one that integrates data from across an existing IT landscape and includes data from legacy systems and disparate instruments, enables clinical reports to be generated automatically based on results from various diagnostic processes or departments, accelerating the reporting process. Again, via a clinician’s portal, these reports can be automatically delivered back to the doctor, further improving the TAT of the lab.

End-to-end operational efficiency

High sample volumes, preanalytical mistakes, and complex workflows are some of the primary hurdles that diagnostic labs must overcome to maintain adequate TAT and ensure patients receive the correct diagnosis and treatment in a reasonable time frame. 

Implementing a modern, configurable LIMS can have a positive impact on every aspect of a laboratory, including sample accessioning, order processing, lab workflow logistics and distribution, instrument integration, reporting, and compliance, by orchestrating the different components of the diagnostics process. 

The LIMS can expand and automate processes, guarantee precise sample management, data integration, and analysis, increase operational efficiency, and drive down TAT.