Precision Medicine: The Next Generation
Preparing your laboratory for a rising tide of diagnostic tests
David Fenstermacher | | Opinion
Next-generation sequencing (NGS)-based diagnostics are overtaking traditional approaches in a wide variety of indications, including infectious diseases, rheumatology, transplants, human hereditary disorders, and non-invasive prenatal testing (1). Increasingly, NGS technologies are also used for the molecular characterization of tumor subtypes, thereby unlocking the use of targeted therapies in early- and late-stage cancers. Add to this the fact that NGS sequencing costs continue to drop, reimbursement is improving, and patients are gaining more education on what’s available to them, and it’s easy to see why the number of available NGS tests is only expected to grow (2).
NGS has reached a turning point in diagnosing and treating rare and inherited diseases, which are often difficult to identify clinically. In these complex diagnostic cases, performing whole exome or genome sequencing can detect these rare diseases sooner and direct care appropriately. As the cost decreases and performance improves, more payors are seeing the benefit of preventing expensive and unnecessary tests and avoiding treatment delays. Indeed, diagnostic testing for rare diseases is one of the fastest-growing market segments (3).
Perhaps you have already had to respond to the rapid rise in genetic testing. But are you satisfied with your solutions? Are you confident that they will scale to meet future demands for turnaround time, quality, and accuracy?
The first step for any NGS provider, if you haven’t already taken it, leverages another major technological advance: the cloud. Moving your NGS analysis to a cloud-based informatics platform provides an environment that can flexibly scale to meet the demand for increased test volume, while saving time and money. Cloud-based systems enable you to optimize analysis pipelines for quality, speed, runtime, and cost, and can help eliminate bottlenecks in processing queues and server capacity.
If you are looking to expand your footprint, either locally or globally, the cloud can help bring your production pipelines into a single, unified environment, with version-controlled updates rolled out simultaneously across your locales. The cloud-based systems also allow you to decentralize your sequencing among multiple sites or global lab partners, and ensures compliance and intellectual property (IP) protection by keeping your proprietary pipelines centralized and secure in your home region.
Of course, IP is not the only thing you have to protect. Make sure your cloud-based informatics platform has version-controlled tools that allow team members to share large datasets and analyses securely and efficiently, with encryption and tracking to ensure auditability and reproducibility. Ideally, the platform will also facilitate easy compliance with the industry’s strict privacy regulations, which are constantly changing and often vary by region. However you choose to develop your informatics approach, you will always have to consider security and compliance – so keep them in mind from the start to avoid trouble down the line.
For a quick “informatics health check,” ask yourself the following questions:
- How will the changing genetic testing landscape impact my operations and support needs?
- Is my informatics system sufficient?
- Is it scalable?
- Does it give me the flexibility I need?
- How does it handle quality, security, and compliance?
- Can it help me improve my sample turnaround time or pipeline development?
With the coming deluge of genomic tests in the next five years or less, how can you ensure you’re making the right investments today? Should you continue building your own infrastructure or upgrade to a purpose-built NGS informatics platform?
Consider the growth you anticipate in the next few years and the impact on your existing systems. Also consider the hidden costs associated with managing your own NGS informatics infrastructure. For instance, slow compute times, backlogged queues, and cumbersome processes for accessing test data create bottlenecks that can increase your turnaround time. And don’t forget the opportunity costs you lose by tying up your resources and headcount on software development. Do you want to continue to invest time, money, and people in operating, scaling, maintaining, securing, and providing support on genomic analysis infrastructure? There are clear benefits to keeping the process in-house – but don’t underestimate your own need for support, and don’t hesitate to call on it when necessary. By keeping pace with technology and industry innovations in the NGS and genomics field, you can ensure that you are not only ahead of the tide, but making your own waves.
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- C Di Resta et al., “Next-generation sequencing approach for the diagnosis of human diseases: open challenges and new opportunities”, EJIFCC, 29, 4 (2018). PMID: 29765282.
- KA Phillips, MP Douglas, “The global market for next‑generation sequencing tests continues its torrid pace” (2018). Available at: bit.ly/37k2nWi.
- Concert Genetics, “The Current Landscape of Genetic Testing – 2018 Edition” (2018). Available at: bit.ly/2KDmKEc.