Future-Proofing Your NGS Clinical Diagnostic Lab & LIMS

In my previous post, I described the complex challenges NGS Clinical Diagnostic laboratories face because of legacy software.

To recap, these include limitations in usability and efficiency, higher costs than labs generally understand, the difficulties that arise when you need to replace key personnel, and the lack of specialized software expertise in internal development teams.

For laboratory and technical leads who want to future-proof their business with a solution that is more agile, scalable, and usable, I propose considering the following actions.

Reframe Costs

Traditional thinking about return on investment (ROI) still applies in this new paradigm. When you can account for all the costs and benefits of the decisions you have made, you will be in a better position to make choices about your direction in the future. Don’t forget to include the cost of implementing and running the system, the cost of ongoing updates and changes (particularly those related to new processes and regulations), and the cost of personnel.

Also, consider framing cost around the value you can provide your clients or customers, how it will enhance the relationship you have with them, and the ROI you will see for this added value. Think about what it’s worth to your customers if you can provide faster turnaround time, more accurate reporting, or more comprehensive analysis. And factor in the idea that errors, lost orders, incorrect results, and rework can all have large hidden costs. In my experience, these are often missed opportunities for adding value.

Consider the Complexity of Requirements

Labs might think they understand their current system, but existing systems often contain undocumented functionality with implied requirements. There’s a big cost in duplicating these hidden functions. Replacing an existing system is one of the hardest things there is. Users are willing to accept missing functionality on new systems, but they expect replacement systems to support every feature in the existing system on day one. This is especially true if you’re trying to grow the business by scaling-up processes. Having a clearly defined set of requirements is an absolute must.

Revisit Custom Software

Allow yourself or your team to rethink the way software is built and maintained. In the short term, a custom solution can seem like the best way to solve your lab’s complex requirements. But if you’re focused on growing the business, your system needs to be built for change and scalability so that you have more agility in response to the changing market.

Key questions to ask yourself about your existing custom software include:

  • Have your software demands evolved beyond your internal capacity?
  • Will you need to increase spending to support and retain specialized LIMS developers?
  • Would your internal developers be better deployed on different parts of your business systems (bioinformatics, customer-facing software, etc.)?

Software development teams are no stranger to team and scope changes, so don’t be afraid to make the adjustments you need to meet current and future business requirements.

Factor-In Ongoing Maintenance

It’s generally agreed that adopting a commercial-off-the-shelf (COTS) LIMS will reduce your need to support a development team to implement and maintain LIMS. A COTS LIMS can free-up your internal developers so they can focus on creating valuable new pieces of business software or improving other mission-critical challenges in your organization. However, you need to be realistic about the effort your team has to invest over time to maintain even a COTS LIMS. Working with our clients, I’ve seen that cost as much as 25% of the initial investment.

Respect Data

Don’t forget about the data in the existing system. Everyone knows that data is an asset, but you can only tap into its true value if it’s accessible. Often labs don’t recognize the wealth of information they have stored in their legacy systems—information they could be sharing with ecosystem partners and others in the life sciences community to improve patient outcomes.

If you’re planning to upgrade your legacy software, questions to ask include:

  • How will you migrate data?
  • How will you maintain the integrity and utility of the data in the new data structure?
  • What will your team do during migration?

Build the Right Stakeholder Team

A critical part of upgrading any software is including the right people during decision-making. When you have the right people on board, you get the insights you need to ensure everyone’s needs are met. It’s also a great way to get buy-in for new workflows and vital for successful change management.

I recommend including some or all of the people in the following positions:

  • Laboratory director. Accountable for the day-to-day running of the lab, the laboratory director can help align business strategy with current and future workflows.
  • CEO or head of the organization. In charge of the company’s business direction at the highest level, the head of the organization needs to understand the various options and weigh-in on what makes the most sense for the business as a whole.
  • CFO or budget-holder. Has a high-level strategic awareness of what needs to be in place for this type of spend.
  • Director of Quality and Regulatory Affairs or head of quality of the organization. Understands the regulatory environment and what needs to be done to achieve and maintain accreditation.
  • IT or operations. Knowledgeable about both software development and software support.
  • Medical/scientific managers. Accountable for the final results from the clinical lab.
  • Computational biologists. Oversees the in-silico analysis, results, and often reporting.
  • Technical/software leads. Understand the details of the software and why decisions have been made in the past that have led to the current state.
  • Software users. Use or update the software and offer an end-user perspective on efficiency and key features.
  • Sales/customer success/business development. Aware of the lab’s ability to sell to and retain clinic and hospital customers.

I also advise labs to be generous with decision-making time. Rushing through workflow changes can lead to costly mistakes and dissatisfied stakeholders and customers. Above all, you need to ensure that adding new tests or products is feasible. And remember that letting the right people give input leads to greater job satisfaction and less staff turnover.

Determine a Realistic Budget

Finally, don’t underestimate the cost to re-implement or upgrade your current system. A realistic budget based on clearly defined requirements has to be a non-negotiable first item on your to-do list. Without it, you’re dooming the team to face the same implementation challenges again in the future.

Remember that the existing system may include undocumented requirements and undocumented interfaces to other systems. Requirements are difficult to identify, even when you’re replacing an existing system. You need to think through what happens to data in the existing systems. What access do you need to the information? Does the information need to be visible in the new system? What happens to information in flight or already published studies and in-production assays? Also, it can be tempting to try and fix all the limitations of the existing system in one enormous project. This can easily lead to failed projects which are perennially “almost done” but never make it into production.

None of these are easy decisions which is why we recommend working with a partner to ease the transition. If there’s one thing we’ve learned from our work in the industry, it’s that laboratories have to be able to update processes and workflows rapidly, scaling up or down to meet demand. Is your lab in a position to do that? If not, we can help.

Mark Swinkels is co-founder and CTO of Semaphore Solutions. Mark has led some of the largest NGS LIMS implementations in the world.