Consider this: your company has decided to bring on a new next-generation sequencing (NGS) assay, and you are tasked with bringing it onboard in your lab with urgency. This is the very situation the customers we work with daily are facing. Very often, the timeline for launch has been predetermined without understanding all the considerations that need to go into ensuring the project has a successful outcome. We have seen NGS launches take as little as four months, or span four years, sometimes with the same assays and goals. And why is this?
There are many variables that play into the success of NGS being adopted in any lab, whether for research or for clinical use. As a result, at the beginning, there can be many unexpected and costly delays. Based on our experience and expertise, we have identified five criteria to consider in order to successfully launch NGS in your environment.
Whether you are building out a GxP pipeline, clinically validating an LDT, or verifying an IVD, understanding what is needed from a regulatory perspective at the end of your launch will allow you to design a comprehensive project plan that covers all requirements upfront. This also allows you to gain efficiency by designing your experiments to accomplish multiple goals – two birds, and one sequencing run. Taking the extra time to thoughtfully plan will save time and money, because your final product will not have gaps in addressing regulatory requirements, which are costly to address later. Whether it be not considering audit logs, the full scope of regulatory paperwork needed, or using the incorrect number or types of samples – all of this can be avoided by starting with the end in mind.
While this may seem self-explanatory, in practice, we have seen that 85% of project delays are due to wet lab quality issues due to inexperienced staff. This also leads to a high degree of turnover, with 20% of projects getting further delayed due to lab staff attrition. NGS assays are complex wet lab experiments that require a high degree of technical acumen. It is common for inexperienced technicians to struggle for several months as they navigate this learning curve. For even more niche NGS such as chromatin immunoprecipitation sequencing or single-cell RNA-sequencing, the number of variables that are required to fine tune prior to even starting the library preparation increases, as does the needed skillsets of your lab technicians. If there is a high degree of urgency to launching your test, be specific in your job descriptions and hire technicians who have experience with the type of NGS you are bringing onboard.
Thorough research into the design and content of available assays and what they do or do not test for, and aligning that to your intended purpose, is critical to the success of any NGS assay. For instance, if you are a clinical laboratory and expect a substantial portion of your patient population with a diagnosis of non-small cell lung cancer, you would want to ensure your assay can detect tumor mutation burden. This biomarker is clinically relevant for pembrolizumab to the patient population you intend to serve and directly impacts your potential for reimbursement. Ensure you are looking at what the data needs to give you, to ensure you have factored that into your assay selection or design. Incorporate this into your business plan, a must have, to ensure that the cost to run your assay versus the reimbursement rate will be profitable.
In research and development, bioinformaticians frequently develop and design their secondary analyses locally, and then lift this over to a cloud computing production-level environment. Because of this, incompatible formats or languages, unsupported bioinformatic tools, and variant call formatting - all can be obstacles that need to be overcome. If you design with these dependencies in mind, implementing your final workflow to your production-level environment will be significantly easier.
While our previous tips revolve around the design and implementation of your NGS assay, this often-overlooked topic addresses a key critical element to scalability after go-live: automation. Whether you are performing large data analyses for an R&D study or expecting increased samples being ordered through your lab test, using software integrations and automated processes helps eliminate common human errors, reduce time to analysis, and create robust scalable solutions to support your operations. While automation can often be handled as phase two of a project, if you plan to scale quickly you should consider it from the beginning, as these projects often require technical non-lab resources.
These five key considerations are at the heart of how we engage with our customers. Our team of experts recently redesigned our engagement methodology based on the analysis of 180+ customer onboardings and created a simple decision tree that helps us guide customers around potential pitfalls. Bringing on an NGS assay is challenging work, and when deadlines and budgets are not built with these factors considered, we often see our clients have this as additional stress. Whether new to NGS or adding a new assay, understanding and planning for these key considerations meets our customers where they are in terms of readiness, planning, and end-goals, and to create comprehensive project plans that ensure success.
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