Introduction
Next-Generation Sequencing (NGS) demands precision and efficiency, but manual library preparation introduces variability and slows down workflows. Errors in pipetting, reagent handling, and sample tracking can impact data quality and reproducibility.
Automation addresses these challenges by standardizing processes, reducing hands-on time, and increasing throughput. This article explores how NGS automation improves library preparation efficiency and accuracy.
Importance of Automating Library Preparation in NGS Workflows
Automating NGS library preparation significantly improves efficiency, accuracy, and reproducibility in sequencing workflows. Manual sample handling and pipetting introduce variability, which automation eliminates by ensuring precise reagent dispensing and sample tracking. This reduces the risk of contamination, pipetting errors, and inconsistencies caused by human handling.
Automation also increases throughput, a critical factor in high-throughput sequencing applications. By minimizing hands-on time, automated systems allow labs to process more samples in less time while maintaining consistency across runs. This streamlines operations and enables researchers to scale their sequencing efforts without compromising quality.
Standardized automated protocols improve reproducibility by eliminating batch-to-batch variations. Manual workflows often introduce subtle differences in reagent handling or incubation times, leading to inconsistencies in sequencing results. Automation ensures that every step follows a predefined, repeatable process, producing uniform library quality across experiments.
In regulated environments, compliance and quality control are essential. Automated tools such as omnomicsQ provide real-time monitoring of genomic samples, flagging those that do not meet pre-defined quality thresholds. This ensures that only high-quality samples progress to clinical analysis, reducing wasted resources and false reports on findings.
Additionally, compliance with ISO 13485 standards and IVDR regulations is critical for laboratories handling diagnostic samples. Automation supports adherence to these regulatory frameworks, ensuring that sequencing workflows meet strict quality and safety requirements. Participation in External Quality Assessment (EQA) programs, such as EMQN and GenQA, further enhances cross-laboratory standardization.
Furthermore, GDPR and HIPAA compliance must be considered, particularly for healthcare and clinical research institutions handling sensitive genomic data. While GDPR and HIPAA focus on protecting patient privacy and data security, IVDR ensures the safety and effectiveness of diagnostic sequencing products.
Lastly, automation enables seamless integration with existing LIMS and IT systems, ensuring smooth data management and interoperability with genomic analysis platforms. This makes it easier for labs to manage samples, track data, and maintain a fully compliant and efficient NGS workflow.
Key Components of NGS Automation
1. Use Automated Liquid Handling Systems
Automating liquid handling is important for improving consistency and throughput in NGS library preparation. Manual pipetting introduces variability, which can compromise sequencing accuracy.
Automated liquid handling systems eliminate these inconsistencies by precisely dispensing reagents, ensuring that each sample receives the exact volume required for optimal library preparation. This precision leads to more uniform sequencing results and reduces the likelihood of failures caused by human error.
Beyond improving accuracy, automation reduces cross-contamination risks, which is critical for maintaining sample integrity. Manual pipetting increases the chance of introducing contaminants between samples, particularly in high-throughput workflows.
Automated systems use disposable tips, controlled aspiration speeds, and optimized workflows to minimize contamination. This ensures that each sample remains isolated, preventing the carryover of reagents or nucleic acids that could lead to false sequencing results.
Automated liquid handling also enhances operational efficiency by streamlining repetitive tasks. Instead of spending hours performing manual pipetting, laboratory personnel can focus on data analysis and process optimization. This shift improves overall productivity and allows for higher sample throughput without requiring additional staffing. Moreover, integrating automation with workflow software ensures that protocols are executed consistently, reducing variability between runs and laboratories.
2. Integrate Robotics and Workflow Software
Automating NGS library preparation requires seamless integration of robotics and workflow software to improve efficiency, accuracy, and reproducibility. By minimizing human intervention, automation reduces variability and ensures standardized protocols across different runs and laboratories.
Robotic systems handle liquid transfers, pipetting, and reagent dispensing with high precision, eliminating inconsistencies caused by manual handling. This not only increases throughput but also reduces contamination risks and reagent waste.
When integrated with Laboratory Information Management Systems (LIMS), automated workflows enable real-time tracking of samples, reagents, and process steps, ensuring complete traceability and compliance with IVDR requirements, which mandate strict documentation and tracking of sequencing workflows in a clinical environment.
To further improve cross-laboratory standardization, participation in External Quality Assessment (EQA) programs such as those organized by EMQN and GenQA is important. These programs help laboratories benchmark their workflows against industry standards, identifying discrepancies and areas for improvement. Additionally, tools like omnomicsQ provide real-time quality monitoring, flagging low-quality samples before they compromise sequencing results.
3. Standardize Protocols for Reproducibility
Standardizing protocols is important for ensuring reproducibility in NGS library preparation. Automation enforces strict adherence to validated protocols, reducing inconsistencies between sequencing runs. Manual processes often introduce variability because of differences in technique, pipetting accuracy, or protocol deviations. Automated systems eliminate these sources of error, ensuring that every sample follows the exact same steps under precisely controlled conditions. This consistency is key to producing reliable and reproducible sequencing data in both clinical and research settings.
For laboratories working with diagnostic applications, compliance with IVDR and ISO 13485 is mandatory. IVDR, established by the European Union, guarantees that in vitro diagnostic products meet strict safety and performance requirements.
Compliance with ISO 13485 ensures that laboratories follow standardized quality management practices for medical and diagnostic devices. Together, these frameworks help laboratories maintain high-quality standards while ensuring compliance with best-practice guidelines from ACMG and CAP, which are critical for genomic diagnostics.
Automated quality control solutions, such as omnomicsQ, assist in maintaining protocol compliance by monitoring genomic samples in real time. These systems flag any deviations from pre-defined quality thresholds, allowing for immediate corrective action before bioinformatic processes or clinical analysis begin. Additionally, participation in external quality assessment (EQA) programs supports inter-laboratory standardization, ensuring that results remain consistent across different facilities.
4. Monitor Quality in Real Time
Ensuring real-time quality monitoring in NGS workflows is important for preventing sequencing failures and optimizing resource use. Automated systems enable continuous assessment of sample quality, allowing you to detect issues before they compromise downstream analysis.
Tools like omnomicsQ provide real-time genomic sample monitoring, flagging those that fall below pre-defined quality thresholds. This prevents low-quality samples from advancing in the workflow. By identifying suboptimal samples or processes early, laboratories can avoid unnecessary reagent consumption, rework, and delays.
Automated alerts further improve quality control by notifying you immediately when a sample fails to meet established criteria. This allows for rapid intervention, ensuring that only high-quality data progresses through the sequencing pipeline. Combined with periodical external quality assessment (EQA) programs, such as those from EMQN and GenQA, these measures ensure cross-laboratory validation, maintaining consistency and adherence to ISO 13485 standards.
Steps to Consider for Implementing NGS Automation
1. Assess Laboratory Needs and Workflow
To implement NGS automation effectively, you have to first assess your laboratory’s specific needs and workflow. Identifying inefficiencies in manual processes allows you to determine which steps would benefit most from automation. Common bottlenecks include sample preparation delays, inconsistent reagent handling, and steps prone to human error. Addressing these pain points improves both efficiency and data quality.
When evaluating your workflow, consider key factors such as sample volume, required throughput, and regulatory requirements. If your lab processes a high volume of samples, automation can significantly reduce turnaround time while maintaining consistency. Throughput demands also influence the choice of automation platforms, as different systems offer varying levels of scalability.
Additionally, compliance with GDPR, HIPAA, and IVDR is crucial. While GDPR and HIPAA focus on safeguarding patient data, IVDR ensures that diagnostic workflows meet stringent safety and performance requirements for regulatory approval. Ensuring that selected automation solutions meet these standards prevents regulatory setbacks.
A thorough assessment of your laboratory’s workflow helps you select automation tools that align with operational goals. By pinpointing inefficiencies and understanding regulatory constraints, you can make informed decisions that improve sequencing accuracy and efficiency.
2. Choose the Right Automation Platform
Selecting the right automation platform is critical to maintaining a cohesive and efficient NGS workflow. The system has to integrate seamlessly with your existing laboratory information management system (LIMS) and NGS pipelines to avoid workflow disruptions and data silos. A well-integrated platform ensures smooth sample tracking, efficient data transfer, and minimal manual intervention, reducing the risk of errors and inconsistencies.
Compatibility with variant interpretation tools is another essential factor. Solutions like omnomicsNGS streamline variant interpretation and classification, ensuring compliance with ACMG, CAP, and industry best practices while minimizing manual intervention. This integration allows you to maintain a streamlined workflow from sequencing to interpretation, ensuring that results are processed accurately and efficiently. Without proper compatibility, manual data transfers between systems can introduce errors and slow down analysis.
When evaluating automation platforms, consider how well they fit into your existing laboratory infrastructure. A system that aligns with your current tools and protocols will support a smoother transition to automation, minimizing disruptions and maximizing efficiency.
3. Train Personnel for Seamless Transition
Transitioning to automated NGS workflows requires more than just installing new equipment. To fully utilize automation, laboratory personnel have to be properly trained in new protocols, software, and compliance requirements. Without adequate training, even the most advanced systems can lead to inefficiencies or errors, ultimately compromising the quality of sequencing results.
Hands-on training is important to ensure staff can operate and troubleshoot automated systems efficiently. This includes:
- Mastering automated liquid handling systems to ensure precise reagent dispensing and minimize sample loss.
- Understanding workflow software to configure protocols, monitor real-time quality metrics, and adjust parameters as needed.
- Understanding GDPR and HIPAA for data security and IVDR, ISO 13485, and ACMG guidelines for ensuring regulatory adherence in diagnostic workflows.
- Developing troubleshooting skills to quickly identify and resolve issues that could disrupt sequencing workflows.
A structured training program should incorporate both theoretical knowledge and hands-on practice. Interactive sessions where personnel engage directly with automation tools improve retention and confidence. Additionally, ongoing training ensures staff stay updated with system upgrades, new compliance requirements, and evolving best practices.
4. Ensure Compatibility with Existing Systems
Ensuring compatibility between automated NGS platforms and existing laboratory systems is critical to maintaining an efficient and compliant workflow. Automated solutions have to seamlessly integrate with current NGS pipelines, bioinformatics tools, and regulatory frameworks to prevent disruptions and ensure data integrity.
Before implementing automation, verify that the system supports key compliance standards. While GDPR and HIPAA focus on data security and patient privacy, IVDR ensures that NGS workflows for diagnostic applications meet strict regulatory safety and performance standards.
Interoperability with quality control and validation tools further strengthens NGS workflows. For example, omnomicsQ enables real-time monitoring of genomic sample quality, flagging subpar samples before they compromise downstream analysis.
Similarly, omnomicsV facilitates the validation of NGS workflows, ensuring that results meet the necessary accuracy and reproducibility standards. Integrating these tools with automated systems ensures compliance with ISO 13485, supports IVDR validation, and enhances cross-laboratory standardization.
By validating automation compatibility with existing infrastructure and ensuring smooth interoperability with essential quality control and validation tools, laboratories can maximize the benefits of NGS automation while maintaining regulatory adherence and data reliability.
5. Evaluate Cost and Return on Investment
Evaluating the cost and return on investment (ROI) of NGS automation is important to making an informed decision. While the initial investment might seem considerable, the long-term savings and operational benefits often justify the expense.
Automated systems reduce reagent waste by precisely dispensing small volumes, minimizing overuse, and preventing unnecessary sample loss. They also increase throughput, allowing more samples to be processed in less time, which improves overall efficiency.
Additionally, automation significantly reduces reruns and failed experiments by improving consistency and eliminating human errors, leading to lower consumable costs and less wasted sequencing capacity.
Beyond cost savings, automation enhances regulatory compliance by supporting IVDR certification, ISO 13485 certification, and adherence to ACMG and CAP guidelines. Automated solutions help labs maintain standardized workflows, reducing audit risks and ensuring reliable diagnostic outcomes. Solutions like omnomicsQ allow real-time quality monitoring, flagging samples that fall below predefined thresholds, which supports compliance with ISO 13485 standards — a prerequisite for IVDR certification. By integrating automated quality control and validation tools like omnomicsV for process validation and omnomicsQ for real-time sample quality monitoring, labs can further improve accuracy, reproducibility, and compliance with regulatory frameworks.
These financial and regulatory factors contribute to a strong long-term ROI, making automation a strategic investment for laboratories aiming to optimize efficiency, reduce costs, and maintain compliance with industry standards.
Conclusion
NGS automation improves both efficiency and accuracy in library preparation. Automated liquid handling, robotics, and workflow standardization reduce variability and improve throughput. Real-time quality monitoring ensures reliable sequencing results while minimizing errors. As laboratories scale operations, integrating automation aligns with both operational and financial objectives. Investing in the right automation strategy supports long-term reproducibility and data integrity, strengthening overall NGS workflows.
Euformatics is a leading provider of advanced genomic data analysis solutions, helping laboratories enhance the efficiency and accuracy of their NGS workflows through automation. With tools like omnomicsQ for real-time quality monitoring, omnomicsV for validation, and omnomicsNGS for variant interpretation, Euformatics enables seamless integration, regulatory compliance, and high-performance sequencing.
To simplify budgeting for NGS validation and automation, Euformatics offers a transparent price configurator that allows laboratories to customize solutions based on their specific needs. Explore the Genomics Hub price configurator to find the best automation strategy for your lab.
Book a demo today to see how Euformatics can optimize your NGS automation workflow and improve data accuracy.
FAQ
What Are the Key Benefits of Automating NGS Library Preparation?
Automation improves efficiency, accuracy, and reproducibility while reducing hands-on time and errors. It ensures consistent results, increases throughput, lowers costs, and optimizes reagent usage. Walk-away workflows free up researchers for other tasks.
How Does Automation Minimize Errors and Improve Accuracy in Library Prep?
Automation reduces manual handling, ensuring precise reagent dispensing and standardized workflows. This minimizes contamination, pipetting errors, and inconsistencies, leading to reliable sequencing results with higher data integrity.
Which Steps in the NGS Library Preparation Workflow Can Be Automated?
Automation can streamline DNA fragmentation, end repair, adapter ligation, size selection, amplification, and clean-up. This reduces errors, improves reproducibility, and increases sample throughput using robotic liquid handling and integrated platforms.
What Are the Different Automation Platforms Available for NGS Library Prep?
Automation platforms vary in throughput and flexibility. Options include liquid handling robots and integrated systems. High-throughput platforms suit large labs, while benchtop models fit smaller workflows. Choosing the right one depends on lab needs and budget.
How Can I Integrate NGS Automation Into My Existing Lab Workflow?
Start by assessing current workflows and identifying bottlenecks. Choose automation solutions that fit sample volume, reagents, and data management needs. Training staff and ensuring seamless integration improve efficiency, accuracy, and reproducibility.
References
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- Endrullat, Christoph, Jörn Glökler, Philipp Franke, and Marcus Frohme. “Standardization and quality management in next-generation sequencing.” Applied & translational genomics 10 (2016): 2-9.
- Hess, Jacob Friedrich, T. A. Kohl, M. Kotrová, K. Rönsch, T. Paprotka, V. Mohr, T. Hutzenlaub et al. “Library preparation for next generation sequencing: A review of automation strategies.” Biotechnology advances 41 (2020): 107537.
