Essential LIMS Features for Efficient COVID-19 Sample Management
During the current pandemic, the ability to rapidly acquire, test, and report samples for the novel coronavirus has been essential for labs’ survival. Every COVID-19 testing lab demands a Laboratory Information Management System (LIMS) to coordinate the huge influx of samples. For any lab to quickly test and report samples, their sample management software must have certain features to facilitate rapid testing. (Read: What is a LIMS?)
These eight features of a sample management LIMS ensure your lab can easily and quickly handle a large number of COVID-19 samples.
Essential LIMS Feature #1: Highly Secure, Cloud-based, Accessible Anywhere on Any Device
A variety of people will need to access your laboratory’s sample management software: physicians and nurses, laboratory testing personnel, management, and directors. The ideal solution is a cloud-based system they can all access on any internet-connected device.
A cloud-based LIMS can also be highly secure, able to manage any form of Protected Health Information (PHI). In fact, a large number of cloud-based systems currently store and process PHI every day, approved by and compliant with all pertinent regulatory agencies. To ensure PHI security, the LIMS system should absolutely require two-factor authentication (2FA) for anyone that accesses PHI.
Essential LIMS Feature #2: An Interface for Physicians to Order Tests and Review Results
Here’s a nightmare for testing labs: The lab knows about a sample only when it shows up at their lab (known as “bluebird” samples, as they appear “out of the blue”). You can’t properly staff a lab if you do not know the number of samples that require testing on any given day. When each sample arrives with a paper test request form, laboratory technicians must enter all sample information from that paper form.
The process is extremely cumbersome and error-prone. Reading paper test request forms is a common challenge due to poor handwriting, poor quality printing, or damage during delivery. Many samples suffer significant testing delays from errors caused by lab staff forced to enter data directly from test request forms.
Improving the sample testing order process
There’s a far more accurate, efficient process. A sample test is ordered prior to the physician or healthcare provider shipping the sample. This advance order occurs through a special interface in the LIMS, such as a portal specifically for physicians or healthcare providers. With this process, the laboratory gains efficiencies by knowing the number of samples that will require testing on any given day. Lab staff need only to verify that the information on the test request form is consistent with the information entered into the LIMS.
Finally, if the LIMS is a cloud-based system (see feature #1), any physician or provider can easily order a test from any healthcare facility or sample acquisition location, such as various drive-through sample collection tents.
Essential LIMS Feature #3: Batched Sample Processing, Including Liquid Handlers
Some available technologies make it extremely easy to test a single COVID-19 sample (such as single sample-single-use PCR amplification systems). But these systems are expensive for a single sample, and can generally only test a few samples per hour.
Any lab serious about performing COVID-19 testing can test hundreds of thousands of samples a day. To meet this throughput, the laboratory must have a sample management system that can process 96-well or 384-well plates that are full of samples.
The ability to simultaneously process 96 to 384 samples can require significant computation resources. A COVID-19 testing LIMS must be able to handle this volume and process the appropriate controls concurrent with each sample.
Each lab may choose to batch samples differently or use different controls. Therefore, the LIMS must have the flexibility to be configured to the needs of each individual testing lab. This includes processing data files from different liquid handlers or qPCR instruments. Data files from each liquid handler program will likely be formatted differently, adding to the complexity the LIMS must be able to manage.
Essential LIMS Feature #4: Automated Data Analysis and Result Generation
Each testing lab generates raw sample data from different instruments. Each file has its own unique format and sample naming conventions. The LIMS must absolutely be able to properly harvest this data. Ensuring that all data is accurately associated with its correct sample can be a tricky process, especially since most COVID-19 tests generate multiple data points for each tested sample (e.g. CT values for the three SARS-CoV-2 genes, and a CT for a spiked internal control).
After all testing data is appropriately associated with each sample, the LIMS should instantaneously analyze the sample and generate a result. The data auto-analysis can be exceptionally complicated. The LIMS must first assess all controls that are run with samples. Then the LIMS assesses the sample itself. Finally, it reviews the possible re-testing data if a sample is run multiple times (see feature #8 below). While some testing workflows use vendor software for raw data analysis, all values from analysis must still be accurately imported into the LIMS, and all re-testing values analyzed.
Essential LIMS Feature #5: Result Review and Automated Report Generation and Delivery
After a the LIMS generates a sample result, a laboratory director (or other appropriate staff) must review the data. Considering the limited time these lab personnel usually have each day, it is paramount that they can review results for each sample easily.
They should be able to conduct the review of all negative samples in batch. Once the sample data are reviewed and approved, the LIMS should automatically generate a report. To prevent errors and save time, lab staff should never have to create a manual report, under any circumstances. The LIMS should always generate each sample report, even for amended reports.
All positive samples will likely require critical calls to the physician, healthcare provider, and/or patient. The LIMS must be able to easily and quickly document each critical call. If the LIMS also provides contact information for each individual sample — the contact may be different for each positive sample — that can be extremely helpful.
Finally, the LIMS should automatically deliver each report to the proper physician or healthcare provider. This delivery can take many forms, including a secure email or electronic fax, or by posting to the portal.
Essential LIMS Feature #6: Queue-based Sample Tracking
Any serious COVID-19 testing lab will process hundreds or thousands of samples in a single day. For those labs, sample tracking can feel like a massive traffic jam. Lab staff must act as traffic cop while also taking responsibility for testing samples. Sample sheets, such as an Excel document, are commonly out-of-date and full of inaccuracies. This leads to poor turnaround time for sample testing and potentially “lost” samples during the testing process.
A good LIMS provides an easy solution: the ability to track all samples in a queue-based manner. Queue-based sample tracking places every sample onto a list, based on that sample’s current status. As each sample is processed, the LIMS should automatically update its status, and push the sample to the next queue.
This queue-based system is perfect for high-throughput sample testing. No sample leaves a list until its status is updated — you can never lose or accidentally forget any sample. Every sample remains on the queue until it is tested.
Essential LIMS Feature #7: Re-testing of Invalid or Inconclusive Samples
All testing labs understand that samples frequently fail and require re-testing. Unfortunately, sample re-testing can be a messy process. Do you create a new sample record for the re-test or overwrite the first sample’s data? Do you have to put a new barcode on the sample to re-test it? Can the data auto-analysis manage re-test results?
A LIMS must address these re-testing problems in a COVID-19 sample testing environment. It is usually not acceptable to simply overwrite initial failed sample data, so the LIMS must generate a new sample record for re-testing. Each re-test record must be appropriately updated during the re-testing process, making sure the original sample record isn’t accidentally updated. The data auto-analysis must be able to accurately calculate a final patient result, accounting for all sample testing results.
Finally, few labs will run re-test samples in a separate batch. The LIMS must be able to process both original sample tests and sample re-tests at the same time.
Essential LIMS Feature #8: The Ability to Report to Public Health Departments
There is one final task after your COVID-19 lab completes all sample testing and reports all results. The lab must report each result to the appropriate Department of Public Health (DPH). Each DPH requires different information on the sample, within different timeframes.
To help the lab facilitate these challenging demands, the LIMS should export all recent results in a format that can be directly provided to the appropriate DPH. Even better, the LIMS might directly integrate with the DPH system. When integrated, the LIMS can automatically send the data in the requested timeframe and format (such as HL7 formatting).
Summary: Essential Features for a COVID-19 Lab’s Sample Management Software
Evaluating a LIMS to manage samples in a COVID-19 testing lab can be tricky. You’ll find plenty of potential features in a LIMS that may not deliver value. Consider the key features listed here as essential. Without them, you’ll be stuck with an inefficient, error-prone sample management system — and frustrated users spending an excessive amount of time managing sample data.
Which LIMS features are essential for your lab? Here’s a quick checklist.
1. A cloud-based system anyone can access, on any device, from any location. It should be highly secure and use two-factor authentication to protect PHI.
2. An interface for physicians and healthcare providers to directly enter information and order tests. This helps you know the number of samples are ordered for the day and prevent errors from manual entry.
3. The ability to handle large batches of samples, such as multiple 96-well plates or a 384-well plate. The LIMS should also manage all types of files generated by your liquid handlers.
4. Automated data analysis and result generation. After data are appropriately imported to each sample, the LIMS should automatically analyze the sample to generate an accurate result.
5. A quick and easy workflow for appropriate personnel to review and approve results. Reports should then be automatically generated, and delivered to physicians and healthcare providers.
6. The ability to easily track the current status of all samples being tested, preferably using a queue-based method. This ensures you’ll never lose or temporarily forget samples during testing.
7. A simple mechanism to re-test samples, allowing you to process new and re-test samples concurrently. Data auto-analysis must specifically handle original and re-test testing data.
8. An easy way to report all relevant sample results to the appropriate Department of Public Health. This can be via an exported, emailed file or full integration, in which result data are sent automatically.
Contact us today to see how Lockbox LIMS can provide COVID-19 support to your lab.