Choosing the Best LIMS for Your Molecular Diagnostics Lab

When molecular diagnostic labs select a laboratory information management system (LIMS), they typically consider the documented list of features and benefits, as they should. Each LIMS has its strengths and weaknesses, so it’s important to consider these when assessing which system best meets the lab’s unique requirements. However, we’ve seen labs regretfully overlook a number of other factors that can have lasting consequences on their efficiency and profitability.

Beyond the basic features & benefits

Labs tend to evaluate a LIMS based on how efficient workflows are, whether the software interface is user-friendly, and what throughput rates are supported. We encourage our clients to also keep in mind these six additional items:

  • Regulatory support. Does the LIMS support your lab’s regulatory regime? Traceability is critical for regulated labs. Most LIMS have an audit trail, but a more important consideration is whether you can produce the reports you need from it easily. The real value of an audit trail is that it lets you solve problems and answer questions based on the underlying data. This is normally achieved through a searching/reporting mechanism.
  • Customer support. Is a qualified support team available during the hours your lab operates to promptly address the technical issues you have? Or is the support team only able to field requests and forward them to a different team to address during business hours? If so, can your lab tolerate waiting for support? Consider how a critical issue with the LIMS will impact your operations.
  • A community of peers. Is there an active community of users? A LIMS that supports such a community has the advantage of allowing you to ask neutral parties questions and draw on a large body of knowledge.
  • Extensibility. Can the LIMS be extended easily by your team or third party consultants? If the vendor is the only one that can extend the LIMS, you might have to wait a long time for your customizations. Remember that every additional instrument, system, or tool probably requires an integration bridge, which requires its own support. Do you have developers and consultants on hand who can help? If not, you’ll have to factor in the learning curve for hiring new developers—in our experience, that could be as high as six months. You’ll want to do a cost-benefit analysis to decide if that money could be better deployed elsewhere in your organization.
  • Costs. There are hidden costs with every LIMS. License fees are a relatively small portion of what it will cost to get it up and running in your production environment. There’s also maintenance and the cost of integrations and training over and above any professional services required to configure it for your lab’s workflows.
  • Vendor lock-in. How easy would it be to switch to another platform if you must in the future? Be sure to examine whether the data can be exported in a standardized format so it can be imported into future systems.

Advanced features that are often overlooked

That said, there are also several advanced LIMS features that can make all the difference to lab operations in terms of efficiency, scalability, and adaptability. Consider the following:

  • Modeling relationships between sample, patient, and order. Many LIMS are sample-centric (designed to handle samples and derivatives but not track patient or order information). Clinical labs usually need to track patients, patient relationships, or subjects.

    Some questions to ask yourself include: Can you maintain the hierarchy of sample, patient, and order? Is the relationship fixed, and will it work for you? Can patients and samples be organized into the necessary groupings (e.g., probands and family groups) or research cohorts such that downstream analysis can accurately produce comparative data for control versus treated groups?

    If you have to jump through a lot of hoops to maintain the hierarchical relationship, tread carefully, as it can have downstream consequences for reporting. For instance, if a sample-tracking LIMS lacks the ability to track relationship hierarchy, you might have to use another system with that capability, which means also building an integration—now there are two systems and an integration to maintain, and added technical complexity. In short, if you have to contort your mental model of your lab to fit the software, then the software likely isn’t a good fit.

  • Compatibility with your molecular diagnostics domain. Does the LIMS support all the requirements your lab has for molecular diagnostic tests? In the genomics space, the LIMS has to be able to handle sequencing tests. Check if it supports features such as rerunning tests (requeues), indexing, pooling, sequencer integration, and sample derivatives. If a sequenced sample is split into thousands of subsequent samples, can your LIMS handle that?

    It’s important to balance risk against usability. While the LIMS should be domain-specific, it also has to be generic enough to support everything you require. Which is to say, be prepared to compromise in some areas.

  • Reporting. Entering data into the LIMS is only useful if you can extract that information in a usable form. The LIMS needs to record and report data for a purpose, whether that’s operational reporting (e.g., How can we improve?) or to meet legal or compliance requirements.
  • Search. The LIMS should enable users to search for samples that entail rework or some other action. For example, does it let you identify all the samples that have failed quality control and allow you to repeat them? Potentially, the LIMS could answer this question through a report, but then you’d have to manually find the samples that need to be repeated, which takes more time and effort.

    Note that search is different from reporting. Where reporting is a static view of the data, searching provides a dynamic view that you can act on within the tool. Many labs don’t know upfront what their use cases will be for searching and reporting, but a neutral third party can help you anticipate what your lab might need.

    A further point to consider about search and reporting: Are these functions being performed on live production data or a time-delayed data store? This is an important factor for high-throughput laboratories looking to manage erroneous samples in real-time.

Selecting the LIMS that is the best fit for your lab requires a clear understanding of your lab’s current and potential workflows, and careful consideration of your long-term business strategy.

Our team has extensive sector expertise, understands the various regulatory reporting requirements, and has strategies to mitigate the risks you might encounter when integrating components with the rest of your software stack—so you can focus on other business priorities. If you’d like assistance with the LIMS selection process, contact us today. Or check out our other posts to learn more about the complex software challenges facing NGS clinical diagnostic labs.

Eban Tomlinson heads up Business Development at Semaphore Solutions. Eban leverages his deep technical informatics expertise combined with clinical genomics and genetics project experience to help Semaphore redefine the field of clinical laboratory informatics.