July 25, 2024 · Author: Third Wave Analytics

The Power of LIMS in Streamlining Laboratory Workflows

A Laboratory Information Management System (LIMS) can be the perfect solution to track all of your lab’s activities. These laboratory software systems are specifically designed to alleviate the painful tasks involved with sample testing. Below, we’ve highlighted ways a LIMS can make your laboratory workflow management easier and your lab more successful. Here’s what a LIMS can do for you:

Prevents “Interim” Solutions Like Excel and Google Sheets from Becoming Permanent

While Excel and Google Sheets can be excellent tools for many situations, there are a myriad of reasons why you should not use these solutions as a replacement for real laboratory information system. Individual Excel files ultimately fail to provide the benefits of a LIMS due to several limitations:

• Anyone can delete or move Excel files or Google Sheets inadvertently
• The number of individual Excel or Google files can explode to dozens or hundreds, forcing you to spend most of your time trying to find the files you need
• Accessing individual files remotely may be difficult or impossible to do in a highly secure manner
• Multiple users cannot always view and/or edit a file at the same time
• Tracking changes can be messy and difficult to manage
• Giving specific users ‘view’ or ‘edit’ access is not easy—or even possible (meaning you need to create more files!)
• Performing calculations for complicated workflows requires lookups and relationships among several different data elements across different files

LIMS offer many features for lab workflow management that go beyond the capabilities of Excel. LIMS support simultaneous access and editing by multiple users, robust security measures to keep your lab data protected, audit trails to show who accessed or modified data and when, advanced sample tracking capabilities including barcodes, and automations to alleviate the daunting (and error prone) task of manual data entry.

Maintains Security for Sensitive Data Like PHI

Many labs manage sensitive data that require high security, including Protected Health Information (PHI) for clinical testing labs and intellectual property (IP) for research labs. Managing user access efficiently in highly secure environments is nearly impossible when using individual files like Excel or Google Sheets.

For instance, PHI must always be kept secure in a HIPAA-compliant manner. This generally requires highly restrictive access solutions such as two-factor authentication, which are impossible to implement when accessing through individual Excel files or Google Sheets. Additionally, if you’re not using appropriate lab software, you may not be able to detect when a breach of sensitive data has occurred. Any inadequacies in your security can result in steep fines or even the forced closure of your lab.

LIMS software is designed with robust security measures that are critical for your lab and company to safeguard its data. Protecting your lab requires a LIMS system that has strict access policies so that only appropriate people have access to data. Furthermore, LIMS software provides insight into which data was accessed, and by whom, with a time stamp marking when that access occurred. Without a Laboratory Information Management system as part of your laboratory workflow, accessing this type of audit information is difficult, if not impossible.

Provides Robust Lab Sample Tracking and Management

The most basic functionality within a LIMS is the ability for your staff to enter sample information and track samples in your lab. This can be the most difficult aspect of lab workflow management and is essential for a LIMS to get just right.

A LIMS system can provide users the ability to accession and enter samples through a variety of methods. Sample accessioning can vary significantly across labs, so your lab should evaluate which LIMS offers the appropriate tools for you. Nearly all LIMS will allow for sample entry via a manual one-at-a-time process. However, some also have additional high-throughput tools for labs to enter samples in bulk. This can include uploading files that have hundreds of samples, or API integration with another system.

Once you’ve entered your samples into a LIMS, it is important to track them all using sample barcodes. The right LIMS can use any type of barcode for your samples that you can imagine, and many can even print automated barcodes for you.

Finally, you have to know where your samples are in the testing process. If your lab processes many samples, a queue-based sample tracking tool within a LIMS can really change and improve your lab’s sample management. A queue-based sample tracking tool ensures you never lose samples in the testing process, and that your lab tests all samples in a timely manner.

Prevents Errors During Sample Testing

Any lab’s sample testing protocols can be complicated, especially with workflows for NGS labs or clinical sample testing. This is where a lab workflow management system can make the difference between success and failure. Some workflows can take days to complete, and may require different people working together to process samples. Every single step must be performed accurately—otherwise you can waste your time and expensive reagents.

Whenever technicians test samples, it is imperative that they have an accurate and up-to-date protocol. A LIMS can display step-by-step instructions from the current SOP to ensure correct protocol is always followed. Within a LIMS, you can quickly update the protocols with a new version and retire older versions, making sure technicians always use the current protocol.

Some complex workflows can take days to complete and require different people to perform individual steps. During sample testing, even a small miscommunication can quickly snowball into a catastrophic mistake. The solution is a good LIMS: Users can mark the steps they’ve performed during sampling, and on which samples, quickly and easily. Then as other users join the process, they know exactly where to pick up on the sample testing. When a lab uses a LIMS to facilitate communication and coordination of sample testing, easily preventable errors can simply evaporate.

Automates Sample Management

Some laboratory workflow management suffers when manual work is part of the process. A LIMS can help your lab greatly improve the efficiency and accuracy of your sample testing workflow by automatically performing certain steps that personnel usually perform manually. Automating this work will save time and prevent errors.

Automated Sample Processing Calculations

Most sample testing workflows involve a few steps in which technicians must perform tedious or difficult calculations. This may include calculating Mastermix volumes, input normalization volumes, or library pooling volumes in an NGS workflow. To expedite the process and prevent costly errors, your lab can have LIMS software perform all these calculations for you.

Automated File Generation

A LIMS can also automatically generate files needed during sample testing. For example, a LIMS can generate a sample sheet directly for input into your NGS sequencer or sequencing analysis pipeline. You can customize and format this file however your lab needs, containing any required data elements.

Automated Tracking of Sample-Specific Data such as Sequencing Library Indexes

Many sample testing processes require in-depth tracking of sample-specific data. Tracking sequencing library indexes, for example, or sequencing libraries within a pool, is one of the most complicated parts of an NGS workflow. We all know the risks of manually tracking complex sample-specific data—and the disaster that can occur during data analysis if the wrong index is associated with a sample.

To alleviate these challenges, a LIMS can help you track complex data such as sequencing indexes. The main goal for using a LIMS during sample workflow is to ensure technicians never have to repeat testing due to simple mistakes like bookkeeping errors during index assignment.

Examples of complex sample-specific automated workflow calculations a LIMS can perform specific to a workflow like NGS:

• Automated assignment of indexes to sequencing libraries
• Tracking all individual sequencing libraries within the pool
• Assessment of clashing indexes when libraries are added to a pool
• Tracking of multiple pools within a sequencing lane/run

Data Capture and Complex Sample Auto-Analysis

Your sample testing workflows can generate a fair amount of data at intermediate testing steps and as a final result. It is important that your lab have the ability to quickly capture, accurately store, and reliably analyze this sample data. It’s common to need access to data from testing that occurred in the past—quick access can save you a lot of time.

Additionally, any automated analysis of raw data will also save your lab time, and prevent errors that occur with manual data interpretation. Therefore, data capture, data storage, and data automated analysis (auto-analysis) are essential functionalities for a LIMS to perform.

Data Capture and Storage

Your lab can quickly and easily upload data from CSV files directly generated by a testing instrument (e.g. quantification instruments). You can store nearly any type of data element in a LIMS, from discrete values to a complex array of data. A LIMS can also store hundreds of unique data values generated during sample testing, with almost no limit to the number of data values that can be captured.

Examples of commonly stored data elements in an NGS workflow:

• DNA/RNA concentrations
• Sequencing library concentrations of either final or intermediate products (e.g. PCR1 or PCR2 products)
• Average fragment size of sequencing libraries
• Molarity of sequencing libraries

Data Auto-Analysis

Automated data analyses of sample data can vary drastically from workflow to workflow. Regardless, it is critical to analyze sample data from any laboratory workflow in a reliable and accurate manner. By using a LIMS, your lab can save the time it takes—and prevent the errors that occur—in performing manual data analysis.

For example, here are types of common data auto-analysis performed during the clinical detection of the SARS-Cov-2 pathogen by qPCR:

• Conversion of raw CT values to a value of “detected” or “not detected” for individual amplicons in each sample/control (e.g. N-Gene, E-Gene, S-Gene, Orf-1ab)
• Analysis to determine if individual controls pass pre-specified Pass/Fail metrics
• Analysis of all controls in a batch to determine if the batch QC is Pass or Fail
• Final analysis of samples to determine if the virus was detected

Inventory and Reagent Management

Many labs want to track the reagents used during sample testing. This may be for regulatory purposes or to help troubleshoot and identify the root of failures during sample testing. Tracking reagents can be an in-depth, complex endeavour, especially when trying to track numerous reagents used during sample testing.

Tracking all aspects of reagents would be nearly impossible without a system like a LIMS. It can help your lab with at least a half-dozen aspects of reagent tracking including:

• Tracking reagent-specific lot numbers and expiration dates
• Tracking the physical storage location of individual reagent bottles/vials/aliquot
• Recording the number of freeze/thaw cycles for reagents
• Calculating reagent usage to know when reagents are running low, and automatically ordering reagents if appropriate
• Tracking individual components with a kit, or the individual ingredients used to prepare a reagent in your lab
• Managing reagent suppliers, quotes, and invoices

Equipment Management

Tracking equipment for a lab is as complicated as tracking reagents. It’s a daunting task that requires managing each individual instrument’s specific needs and complicated schedule of maintenance and upkeep. As challenging as equipment management is, it’s a necessity: your equipment is probably your lab’s single largest financial investment. Managing it well and efficiently is incredibly important for your workflow management process.

Using a LIMS can really save the day when it comes to equipment management. A LIMS can perform all the heavy lifting in your laboratory workflow by taking on the following:

• Recording all equipment-specific “demographic” details such as serial number and model number
• Displaying a schedule with current or future availability and status of equipment
• Reminders for preventive maintenance scheduling and notifications
• Calibration, maintenance, and installation logs
• Logs for daily/weekly cleaning and simple, preventive maintenance (e.g. system washes)
• Deviation or “event” logs for equipment that malfunctions
• Tracking equipment performance over time (e.g. laser signal strength over time for any instrument using LED components)

A LIMS Makes Laboratory Workflow Management Easier For Your Lab

Running a lab is hard. With so much to keep track of during the sample testing process, your lab needs the best-available tools to make your job and life easier. Using a LIMS can provide the greatest impact to do just that, improving the accuracy and efficiency of your lab’s sample testing workflow. A LIMS is an excellent solution whether your lab offers clinical testing, core services, pharmaceutical development, or academic research.

Here’s a recap of the various ways a LIMS can improve your lab operations and deliver a long-term solution for laboratory workflow management:

• Prevents inadequate “interim” solutions from becoming permanent
• Maintains security for sensitive data like PHI and IP
• Provides robust sample tracking and sample management
• Prevents errors through sample testing workflow management and sample processing management
• Gives technicians automated sample management for quick, accurate sample testing
• Saves time and prevents errors with data capture and complex sample auto-analysis
• Inventory and reagent management
• Equipment management, including maintenance and upkeep