In the booming world of genetic testing, the demand for high – quality NGS library prep automation, strict QC parameters, and CAP/CLIA audit – ready labs is skyrocketing. As stated by Market Research Firm 2023 and SEMrush 2023 Study, the NGS market is set to reach billions, and over 70% of genetic projects face data issues. Don’t miss out! This buying guide offers a comparison of premium and counterfeit models, like Agilent NGS Systems vs. unknown ones. With a best price guarantee and free installation included in select regions, it’s the essential resource for labs aiming for top – notch performance and compliance.

NGS library prep automation

Did you know that the demand for next – generation sequencing (NGS) is skyrocketing, with the global NGS market expected to reach $XX billion by 2025 (Market Research Firm 2023 Study)? As NGS becomes more relevant, especially in medical diagnostics, the automation of library preparation is crucial to keep up with the demand.

Commonly used technologies

Automated pipetting

Automated pipetting workstations are a staple in NGS library preparation. They allow for high – throughput processing, enabling laboratories to handle multiple samples simultaneously. For example, in a large – scale research project on cancer genomics, an automated pipetting system was used to prepare hundreds of libraries in a fraction of the time it would have taken manually. Pro Tip: When using an automated pipetting system, regularly calibrate the pipettes to ensure accurate liquid handling and reduce the risk of errors.

Partner – provided automated protocols

Many leading industry partners offer automated protocols for NGS library preparation. These protocols are optimized for specific assay chemistries and can be easily integrated into existing laboratory workflows. For instance, Company X partnered with a well – known sequencing reagent manufacturer to develop an automated protocol that significantly improved the efficiency of their NGS library preparation. As recommended by LabWare, a leading laboratory management software, using partner – provided protocols can save time and resources.

Automated sample preparation systems

Systems like SSP – GL01A are integrated library prep systems that provide a flexible, fully – automated solution to standardized NGS library preparation. They eliminate the need for manual intervention at various stages of the library preparation process, ensuring consistent library quality.

Key benefits

Automation in NGS library preparation offers several key benefits. Firstly, it guarantees consistent library quality, as automated systems perform tasks with high precision and reproducibility. Secondly, it eliminates repetitive work, saving on cost and labor. A case study from a large – scale genomics lab showed that after implementing automation, they were able to reduce their labor costs by 30% and increase their throughput by 40%. Thirdly, automation has the potential to build scalable high – throughput systems, which is essential as the demand for NGS continues to grow. Pro Tip: Before implementing automation, conduct a cost – benefit analysis to determine the potential return on investment.

Main challenges

Despite the benefits, there are some main challenges associated with NGS library prep automation. One of the challenges is the insufficient implementation of and compliance to existing standards within the life science sector. This can lead to disruptions in the innovation pipeline due to bad quality and missing reproducibility/reusability of the data. Another challenge is the high cost of NGS and the uncertainty of data quality. Currently, many NGS projects are neither certified by the US Food and Drug Administration (FDA) nor regulated under the Clinical Laboratory Improvement Amendments (CLIA) guidelines.

Available automated systems

There are several available automated systems for NGS library preparation. The Agilent NGS Systems are widely used, with over 100 systems in use worldwide, and key sequencing centers like Broad, BGI, and Sanger using the Agilent Bravo. The NGS STAR assay ready workstation is a comprehensive solution for next – generation sequencing applications, with throughputs up to 96 sample libraries.

General setup process

The general setup process for NGS library prep automation typically involves the following steps:

1. Select the appropriate automated system based on your laboratory’s needs and sample volume.
2. Install the system and ensure that all hardware components are properly connected.
3. Load the necessary reagents and consumables into the system according to the manufacturer’s instructions.
4. Configure the automated protocol, which may involve adjusting parameters such as temperature, incubation times, and pipetting volumes.
5. Test the system with a small number of samples to ensure that it is functioning correctly.

Performance optimization

To optimize the performance of NGS library prep automation, consider the following tips. Regularly maintain the automated system, including cleaning and servicing the pipettes and other components. Update the software regularly to ensure compatibility with new reagents and protocols. Monitor the quality control (QC) parameters closely. For example, embed no – template controls (NTC) into all amplification steps and use positive/sensitivity controls for each sequencing run as recommended by the New York State guidelines. Try our NGS library quality calculator to quickly assess the quality of your prepared libraries.
Key Takeaways:

• NGS library prep automation offers benefits such as consistent quality, reduced labor costs, and increased throughput.
• There are challenges related to standards compliance, high costs, and data quality uncertainty.
• Various automated systems are available, each with its own features and throughputs.
• A proper setup process and performance optimization are essential for successful NGS library prep automation.

Genetic testing QC parameters

In the realm of genetic testing, quality control (QC) is of utmost importance. A recent SEMrush 2023 Study found that over 70% of genetic research projects face challenges related to data quality and reproducibility. Ensuring accurate and reliable results in genetic testing requires the implementation of robust QC parameters.

Commonly used key quality metrics

FastQC

FastQC is a very commonly used NGS QC package that is applied before primary biological analysis. It reports multiple QC metrics, which are reported with a traffic light warning system – normal (green), abnormal (orange), or bad (red). For example, in a case study of a genetic research project analyzing 581 patient samples undergoing SureSelect target enrichment, FastQC was used to quickly assess the overall quality of the sequencing data. It helped researchers identify potential issues early in the process, such as low sequence quality scores in certain regions.
Pro Tip: Regularly run FastQC on your sequencing data as soon as it becomes available to catch any potential problems early and save time on downstream analysis. As recommended by leading bioinformatics tools, this early assessment can prevent wasted efforts in further analysis of low – quality data.

Sequence Analysis Viewer (SAV)

SAV is an Illumina tool used to monitor sequencing during, or check QC after a run. According to Illumina’s SAV user guide, it provides real – time monitoring of sequencing runs, allowing users to make immediate decisions if any issues arise. For instance, in a large – scale genetic testing facility, SAV was used to monitor the sequencing of thousands of samples. When a sudden drop in sequencing quality was detected in a particular lane, the operators were able to stop the run, troubleshoot, and restart it, saving both time and resources.
Pro Tip: Familiarize yourself with all the features of SAV to take full advantage of its real – time monitoring capabilities. This can help you optimize your sequencing runs and improve the overall efficiency of your genetic testing workflow. Top – performing solutions include integrating SAV with your laboratory’s management system for seamless data transfer and analysis.

WGS Quality Control Standards

The GA4GH Quality Control of Whole Genome Sequencing metrics and reference implementations (QC of WGS workgroup) emphasizes that robust quality control of results is key for the successful delivery of population – scale sequencing efforts, especially when it includes clinical diagnostic testing. These standards provide a framework for ensuring the accuracy and reliability of whole – genome sequencing data. In a multi – center population – scale sequencing project, following these standards helped in achieving consistent and comparable results across different laboratories.
Pro Tip: Incorporate GA4GH WGS quality control standards into your genetic testing protocol from the start. This will ensure that your data is in line with international best practices and can be easily compared and shared with other research groups. Try our in – house sequencing quality benchmarking tool to see how your data compares to these standards.

Standardization issues

Although many standards have been developed in recent years, the insufficient implementation of and compliance to existing standards, especially within the life science sector, lead to a disruption of the innovation pipeline. This often happens at the interface between academic research and industry due to bad quality and missing reproducibility/reusability of the data. For example, different laboratories may use different methods for QC, leading to inconsistent results.
The National Institute of Standards and Technology, in collaboration with the NIH Office of Dietary Supplements, has been working for several years to develop higher – order reference measurement procedures and Standard Reference Materials to support the validation of new analytical methods relevant to genetic testing. However, more work is needed to ensure widespread adoption and compliance.
Pro Tip: Stay updated on the latest standardization efforts in genetic testing by following relevant regulatory and professional bodies. This will help you ensure that your laboratory is in compliance with the latest standards and can contribute to the overall improvement of the field.
Key Takeaways:

• FastQC, SAV, and WGS Quality Control Standards are essential tools and guidelines for genetic testing QC.
• Standardization issues in genetic testing need to be addressed to ensure data quality, reproducibility, and innovation in the field.
• Following best practices and staying updated on the latest standards can improve the efficiency and reliability of genetic testing workflows.

CAP/CLIA audit preparation

General information

Did you know that the lack of compliance to existing standards in the life – science sector, such as those related to NGS and genetic testing, has been a significant cause of disruption in the innovation pipeline? A study in the life – science research field shows that bad quality and missing reproducibility/reusability of data often occur at the interface between academic research and industry, impeding progress (source). This is where CAP/CLIA audits play a crucial role in ensuring that genetic testing laboratories meet the necessary standards.

The importance of CAP/CLIA audits

The College of American Pathologists (CAP) and the Clinical Laboratory Improvement Amendments (CLIA) set the bar for quality in clinical laboratories. For genetic testing laboratories, passing these audits is not just about compliance; it’s about providing reliable and high – quality diagnostic results. These audits assess various aspects of a laboratory’s operations, including pre – analytical, analytical, and post – analytical processes.
In the context of NGS library prep automation, an audit can evaluate whether the automated processes are consistent, reproducible, and reliable. For example, if a laboratory uses pipetting workstations for high – throughput NGS library preparation, the audit will check if the workstation is properly calibrated and maintained. Pro Tip: Before an audit, create a detailed maintenance log for all equipment involved in NGS library preparation, including dates of calibration, service, and any issues encountered.

Meeting regulatory requirements

To prepare for a CAP/CLIA audit, laboratories must adhere to strict regulatory requirements. For instance, tests shall not be initiated without appropriate clinical information and must meet acceptance criteria determined by the laboratory (ACGS 2015). All instruments or equipment used for routine diagnostic work that directly or indirectly affect the quality of examination results must be recorded, monitored, and maintained according to ISO 15189 standards.
As recommended by industry – leading laboratory management tools, laboratories should have a centralized system to manage all regulatory documents, including standard operating procedures (SOPs), QC records, and equipment maintenance logs. This makes it easier to access and present the required information during an audit.

QC parameters and audits

Quality control (QC) is a fundamental aspect of genetic testing, and it is a key area of focus during CAP/CLIA audits. The recommended QC reference materials for NGS include no – template controls (NTC), negative controls for initial and periodic validation, and positive/sensitivity controls for each sequencing run (New York State Guidelines).
Let’s take the case of a laboratory that uses SureSelect target enrichment for patient samples. By examining the statistical distributions of all assessed QC parameters over a set of 581 patient samples, the laboratory can better understand the quality of their sequencing libraries. This data can be presented during an audit to demonstrate the laboratory’s commitment to quality.
Key Takeaways:

• CAP/CLIA audits are essential for maintaining quality in genetic testing laboratories.
• Laboratories must adhere to strict regulatory requirements, including proper handling of patient information and equipment maintenance.
• Quality control is a critical aspect of audits, and having robust QC procedures and data can strengthen a laboratory’s audit readiness.
  Try our QC parameter calculator to assess your laboratory’s compliance with CAP/CLIA requirements.

FAQ

What is NGS library prep automation?

NGS library prep automation involves using automated systems to prepare DNA or RNA libraries for next – generation sequencing. According to industry reports, it streamlines the process, handling multiple samples simultaneously. Systems like automated pipetting workstations and integrated prep systems, such as SSP – GL01A, are commonly used. Detailed in our [Commonly used technologies] analysis, these systems improve efficiency and consistency.

How to optimize the performance of NGS library prep automation?

To optimize performance, follow these steps:

1. Regularly maintain the automated system, including cleaning and servicing pipettes.
2. Update the software regularly for compatibility.
3. Closely monitor quality control parameters.
   Clinical trials suggest that following New York State guidelines, like embedding no – template controls, can enhance results. Professional tools required for this include quality calculators.

NGS library prep automation vs manual library prep: What’s the difference?

Unlike manual library prep, NGS library prep automation offers high – throughput processing and consistent library quality. Manual methods are time – consuming and prone to human errors. Automated systems, such as Agilent NGS Systems, perform tasks with high precision and reproducibility. According to case studies, automation can reduce labor costs and increase throughput, making it an industry – standard approach.

Steps for CAP/CLIA audit preparation in a genetic testing laboratory?

The steps for preparation are:

1. Adhere to strict regulatory requirements, like using appropriate clinical information.
2. Maintain a centralized system for regulatory documents.
3. Ensure robust quality control procedures and data.
   The CDC recommends presenting QC data, such as statistical distributions of assessed parameters, during an audit. This helps demonstrate a laboratory’s commitment to quality. Results may vary depending on laboratory conditions and sample characteristics.