By Alexandra Sommer
Rapid advances in molecular diagnostics, including the application of advanced methods such as next generation sequencing (NGS) in clinical diagnostics, are revolutionizing healthcare. But this puts a lot of pressure on clinical labs to develop, optimize, validate and gain regulatory approval of high throughput assays. The secret to successful automation in the clinical regulatory environment lies in anticipating potential pitfalls.
Anticipation of pitfalls is the secret to success when automating NGS for clinical diagnostics.
Here are seven factors to consider when automating key steps in NGS, such as library preparation:
1. Turnaround time
The expensive and extensive testing involved in modern molecular diagnostics can involve turnaround times from sample to result of as long as two weeks. This puts great stress on the patient and clinical staff, meaning that analytical failure and a re-run must be avoided at all costs. Delays can be critical when the results indicate the need for new, reflex tests. Having automated sample prep that can reliably deliver the throughput and sample purity needed by sensitive analytical methods will maximize efficiency and minimize delays. At the same time, it can ensure more reliable outcomes.
2. Process controls
Next generation sequencing in clinical diagnostics involves many steps, starting with the extraction of highly pure nucleic acid, followed by target enrichment, library construction, sequencing, and bioinformatics analysis. Control throughout this complex multi-step workflow, especially accurate library quantification and QC, is vital for successful template preparation and sequencing.
The application of routine methods with well-defined workflows has traditionally stimulated the development of closed systems that provide almost black-box control of sample to result, minimizing the need for manual intervention – for example in quantitative polymerase chain reaction (qPCR). By contrast, the complexity and variable nature of NGS applications demands a more open automation approach, which increases the importance of implementing procedures that minimize the risk of errors such as sample misplacement, dispensing mistakes, and contamination.
Providing proof of an uninterrupted chain of control under these conditions can be a real challenge. Automating liquid handling with a well-documented and reliable system is a good start. In addition, some of the more flexible open automation systems offer the possibility of pre-developed protocols, as well as in-built control measures and visuals, that can help you “foolproof” complicated workflows.
3. Quality of starting materials
Success with NGS automation in a clinical laboratory depends on a well-constructed library, with optimal yield and quality; minimal sequence bias; and low error rates. Starting with high yield and high-quality materials is the best thing you can do to ensure you get excellent NGS data.
Low sample input will result in lower coverage and a need for more amplification cycles, which increases bias. So ensuring your nucleic acid extraction methods are rigorously controlled using automated methods is a key step to success.
4. Accuracy AND flexibility
The efficient generation of a high NGS quality library generally depends on accurate control over four key steps – DNA fragmentation or target selection, adding adapter sequences, size selection, and finally library quantification and QC. But vendor reagent chemistries are diverse, and their products tend to evolve as new technologies arise. Added to that, you may well need to optimize several protocols such as DNA and RNA library prep and exome target capture.
All this demands a reliable liquid-handling solution that is at the same time flexible enough to accommodate varying applications and protocols. A flexible system will also help you avoid having to purchase and qualify a new platform every time you want to update your approach.
5. Risk of contamination
Careful control over sample handling means avoiding sample cross-contamination and nucleic acid carryover, both within and between runs. To avoid catastrophic contamination, it pays to run workflows in dedicated areas with dedicated equipment and automated platforms designed for contamination-free control over liquid handling.
6. Consolidation to a single platform
In the past, compliant systems were often limited in their throughput, which meant that increasing throughput meant increasing the number of systems in the lab. While having redundant or mirrored systems is recommended as a backup, having several systems means more work for the operators (more daily maintenance and repetitive loading procedures), higher maintenance costs for the labs, and greater lab space requirements. In contrast, consolidating process steps onto a single high-throughput platform can reduce maintenance and labor costs, while freeing up space in the lab for other new technologies.
7. Regulatory considerations for flexible automation systems
Flexible automated liquid handling systems provide an excellent foundation for handling diverse sample types, assays and workflows, and also support future expansion of your assay portfolio. But developing and optimizing assays on these open platforms can create a challenge when seeking regulatory approval. Any liquid-handling platform should therefore minimize the burden of proof by complying with your lab quality management system and standards, as well as meeting the standards of the relevant regulatory authorities. Solutions that have been designed with compliance features built in from the start, rather than tacking them on as an afterthought, will save time and help you avoid regulatory nightmares.
NGS automation in a clinical laboratory can bring more accurate diagnostic methods with shorter turnaround times into play. But as we’ve seen here, the key is to have reliable automation methods.
Want to know more?
Find out more about automation for next generation sequencing.