Next-Generation Sequencing Labs: 6 Critical LIMS Features
In our work with core labs performing next-generation sequencing (NGS), we’ve seen consistent trends regarding the challenges related to lab management, sample management, data management, sequencing workflows, quality control, automation, data analysis, traceability, and the specific functionality needed for life sciences and genomics research and applications.
Because NGS labs perform high-throughput sequencing for the simultaneous analysis of millions of DNA and RNA fragments, a Laboratory Information Management System (LIMS) – also known as a LIMS system – can dramatically streamline NGS workflows, track samples, and help manage NGS data throughout the submission and testing process.
In particular, there can be difficulties when a requester submits their samples and selects all the services they want. To understand what to order and the costs, requesters frequently must have a detailed conversation with the lab. A core NGS lab can find exceptional benefits using a LIMS to guide requestors through submission. By assisting requestors via a LIMS, others in the lab don’t need to set time aside to help.
When evaluating your NGS LIMS, look for the following six key features to help requestors:
- A submission creation portal with tools that accurately guide a requestor through selecting services and provide a template for the process.
- Easy upload of a sample/library manifest.
- The ability to enter billing information securely (e.g. institutional account or grant number).
- Automated estimates of the submission cost (independent from core lab assistance).
- Automated tracking of submission status during lab processing, with notification as critical milestones are reached (e.g. samples are received, sequencing data is available, data sets are processed, etc.)
- The ability to invoice with the submission of the final cost upon completion.
Feature 1: A submission creation portal that accurately guides requestors through service selection.
For many core labs, the most challenging part of managing submissions is ensuring the requestors accurately order the right services. Core labs can offer various services, with complicated caveats dictating which services are available, specific samples, or circumstances. Unfortunately, a requestor may find it challenging to choose the needed services accurately.
A submission creation portal is an essential LIMS feature for a core lab to walk the requestor through each service selection step. This is a guided process, where services are only available for selection based on the requestor’s previous selections. For example, a requestor might first enter the sample type they are submitting and then move on to in-depth questions such as the types of library prep available for that specific sample type.
The outcome is an accurate record of the requestor’s order, consistent and accessible for the lab to review.
Feature 2: Easy upload of samples.
A LIMS designed for core NGS labs provides the requestor with an easy way to upload a list of all the samples in their submission, with each sample’s essential information. It is critical that the requestor accurately provides the details the lab requires for testing, such as sample name, volume, and concentration. The requestor must be able to upload this information easily, and the LIMS must consistently capture it in a way the lab can review.
There’s an essential and complicated nuance about uploading sample information: requirements will likely change depending on the sample type submitted and the services requested. For example, when submitting DNA samples for library preparation and sequencing, the lab may require the volume and concentration; however, when submitting DNA for QC analysis only, the lab may require only the sample name.
It is key that the LIMS has the intelligence to know which information is required for each sample in every scenario. Additionally, the system must be able to verify that the necessary information is indeed uploaded for all samples.
Feature 3: Secure entry and storage of billing information.
Most core labs in the USA allow requestors to pay via institutional accounts or grants. Labs may find they must verify that the account or grant still has resources before commencing work on the submission. It is common for requestors to enter expired funds or grants, which becomes a problem if not identified early in the submission process.
Requestors need the ability to securely enter and store information related to their institutional accounts, grants, or other payments, so the lab can quickly verify the grant or account is in good standing.
Remember that many people at the same lab may have to share the same account or grant for payment. That means multiple system users must have access to the relevant information, but not everyone. The LIMS must be flexible enough to share this information with appropriate users and safeguard it from unauthorized users.
Feature 4: Automated cost estimates for requested services.
One of the most essential processes for a core NGS lab is allowing a requestor to estimate their submission cost after selecting services. This estimate must apply all appropriate rates and pricing for services the user requests. Many core labs have different rates for various types of requestors.
The LIMS must be able to estimate these costs without requiring interaction from lab members. If the LIMS can perform these estimates, the requestor can process their submission promptly without waiting for a lab response. This also saves lab personnel an enormous amount of time.
While this specific LIMS feature is one of the most valuable, it’s also one of the most difficult to configure. All services that can be ordered must be available to the system and kept up-to-date. Likewise, the system must carefully incorporate all logic for pricing scenarios.
Setting up such a LIMS feature can take time. However, it’s worth the investment when requestors can immediately estimate submission costs.
Feature 5: Automated tracking of submissions during testing.
After the lab approves a submission, the lab and requestor must monitor where the submission is in the testing process. Are the samples currently on the sequencer? Or has the lab completed only library preparation? Without a LIMS (or using Excel), requestors typically email lab personnel for a status update, which is distracting and inefficient for the lab.
A complete LIMS designed for bioinformatics and NGS workflows allows the requestor to log in and see the submission quickly. For the lab, this saves time spent on emails. Requestors also benefit from accessing the information they need with just a few clicks.
Finally, a full-featured LIMS can automatically generate emails that proactively alert the requestor when the lab reaches milestones. For example, the requestor could receive an email when the lab receives the samples or when sequencing data are available. If the LIMS sends these emails automatically, lab staff saves even more time.
Feature 6: Invoices sent upon testing completion.
After the lab completes the submission, it faces the juggling act of invoicing. The first challenge for a LIMS is to generate an accurate invoice for services performed—which may differ from the services requested. Getting a precise invoice frequently requires a complete list of costs for all services, and logic related to how the prices were aligned to the specific submission.
Fortunately, a LIMS generally uses the same logic to estimate submission costs and invoices upon completion. Therefore, if a system can accurately estimate submission costs, it can generate an invoice without much extra work.
Most core labs provide services for many requestors, making it complicated to generate an invoice. Requestors can include academic labs, or commercial companies, within or outside their institution. Each requestor type may require a different invoicing process. For some, it may be as simple as deducting charges from an institutional account or grant. Others may require a more detailed process where labs send invoices and await payment information. The LIMS must provide multiple pathways to invoice requestors and record when payment is received for recent invoices.
Summary: Six Critical LIMS Features for a Core NGS Lab
Core NGS labs have plenty to juggle between interactions with requestors and testing of submitted samples. The submission process is particularly cumbersome if requestors ask detailed questions about what to order and the associated costs. If a LIMS can guide requestors to complete the submission process independently, it can be a lifesaver for labs.
What is a LIMS and how can it benefit your core NGS lab? Get a free trial, and see how Lockbox LIMS can be customized to improve your lab’s processes. Just contact our experts today.