Fragment Analyzer Systems

Accurate and reliable next-generation sequencing (NGS) results rely on starting with high-quality samples. In long-read sequencing workflows, such as the PacBio HiFi workflow, essential quality control (QC) steps include assessing input gDNA, intermediate steps throughout library preparation, and the final library. Electrophoretic analysis enables evaluation of sample size, purity, and integrity at each of these steps. Agilent offers several automated electrophoresis systems, including the Agilent Femto Pulse, Fragment Analyzer, and TapeStation systems, each with unique benefits for DNA QC.

This application note demonstrates the capabilities and limitations of each of the automated electrophoresis systems within the PacBio HiFi whole genome sequencing (WGS) library preparation workflow, aiding in the selection of the appropriate QC system.

Formalin-fixation and paraffin-embedding (FFPE) of tissues have long been a cornerstone in pathology for preserving specimens. Chemical modifications that occur during formalin fixation lead to RNA degradation and fragmentation, posing a considerable hurdle for researchers aiming to retrieve high-quality RNA from FFPE samples. Using a quality control system to check RNA integrity after extraction from FFPE samples helps determine if the sample is of sufficient quality for downstream applications such as sequencing.

Explore the capabilities of both the Agilent Bioanalyzer and Fragment Analyzer systems in analyzing FFPE RNA samples using the DV200 score. The DV200 quality metric helps researchers classify degraded FFPE RNA samples by size, determining which are suitable for next-generation sequencing and which are not, saving time and costs. The results provide a comparison between the DV200 scores from each system.

After shifting its focus primarily to long-read sequencing and nanopore sequencing, the team at the Neuromics Support Facility (NSF) in Belgium needed a more robust method for QC analysis. Explore how they utilize the Agilent 5200 Fragment Analyzer system for flexible projects that require the analysis of both DNA and RNA. Discover how switching from the 96-channel to the 12-channel instrument has reduced consumable usage and costs, while increasing flexibility and versatility.

Agilent Technologies compares pre-capture and final libraries on both its Fragment Analyzer and its Bioanalyzer systems with its corresponding DNA assays to demonstrate data equivalency across platforms. Explore the results and find out how reliable and comparable QC results can be obtained from either the Fragment Analyzer and the Bioanalyzer systems, providing ease of mind when gathering data between two labs or transferring QC protocols from one system to the other.

Explore how the Functional Epigenetics Laboratory at KU Leuven in Belgium has integrated the Agilent Fragment Analyzer system into its workflow to maximize efficiency, especially during single-cell nucleosome, methylome, and transcriptome sequencing (scNMT-seq). This technique allows for the simultaneous analysis of chromatin accessibility, DNA methylation, and gene expression within individual cells.

Discover how the lab also uses the Agilent HS NGS Fragment kits with the Fragment Analyzer due to the high-sensitivity analysis, which is crucial for NGS library QC from limited DNA amounts. The libraries often contain minimal DNA after the scNMT-seq protocol, making these kits essential.

Explore the Agilent Fragment Analyzer systems and discover how they can perform both quantitative and qualitative nucleic acid analysis using parallel capillary electrophoresis, and are routinely used in the characterization of in vitro transcribed (IVT) mRNA drug substance (DS) and drug product (DP). Critical quality attributes (CQAs) commonly assessed with the systems include integrity, size, and purity. The systems can also be used to streamline the IVT mRNA CQA workflow, consolidating essential tests for characterizing IVT mRNA onto one platform.

Explore how the TATAA Biocenter, a specialized contract research organization (CRO) in Gothenburg, Sweden, uses the Agilent 5200 and 5300 Fragment Analyzer systems, featuring 12- and 96 channels, respectively, to meet the standards of high sensitivity, specificity, precision, and accuracy. The instruments also enable full sample traceability through integration with the lab’s LIMS system.

Discover how in addition to RNA QC for assay development and biomarker analysis, the Fragment Analyzer systems also play a key role in QC during NGS library preparation, as they are used to determine average fragment sizes, detect adapter-dimer artifacts, and identify over- or underamplification of the library.

One of the main focuses of Hologic Diagenode’s epigenetics department is developing DNA and chromatin shearing devices for short- and long-read sequencing. During DNA sizing and quality analysis, the team opted to use the Agilent Femto Pulse and Fragment Analyzer systems, which can also be utilized for applications such as RNA, chromatin-based methylation studies, and NGS library profiling. Hologic Diagenode explains how its team uses these Agilent systems to achieve higher throughout and greater flexibility in its work, supporting the goal of getting new devices to customers.

In this case study from Agilent Technologies, explore how Kaneka Eurogentec, a contract development and manufacturing organization (CDMO) based in Belgium, produces biopharmaceutical critical raw materials including RNA-based, DNA-based, and protein-based biomolecules. Learn how the company's biomolecules, such as mRNAs, are made in current good manufacturing practice (cGMP) facilities, therefore requiring rigorous quality testing throughout production.

In this application note, Agilent Technologies explains the significance of minimizing adapter dimers in NGS libraries before sequencing. Adapter dimers are formed when two adapters ligate to each other without any insert, leading to erroneous sequencing data. Even small amounts of adapter dimers can cause detrimental sequencing results by affecting library quantification, flow cell loading, clustering efficiency, diversity, and genome coverage. In this note, Agilent's Fragment Analyzer and TapeStation Systems is introduced as a way to accurately and reliably detect adapter dimers below the recommended threshold of 0.5%, providing valuable data to evaluate library quality and make important decisions regarding subsequent analysis.

Jan 21st 2025 - 16:00 GMT / 17:00 CET / 11:00 EST / 8:00 PST

Development and production of IVT mRNA vaccines require measurements of Critical Quality Attributes (CQAs), such as identity, purity, quality, and quantity. Orthogonal methods developed for such purposes are outlined in the USP guidelines for mRNA vaccines.

Agilent Technologies provides many analytical solutions that are used by leading pharmaceutical companies in early-stage drug development through production quality control (QC) and final product release. These systems help users save time and money with optimized workflows, streamlined processes, and fast time-to-results.

Whitney Pike, M.Sc, Application Scientist and Dr. Sonja Schneider, Manager, Application Development, Agilent Technologies, will discuss how automated electrophoresis and LC/MS systems solutions from Agilent provide reliable insights for IVT mRNA workflows at many steps, from QC of the initial plasmid DNA, throughout the IVT process, to the finished mRNA drug product.

Key learning objectives

• Explore QC throughout the entire IVT mRNA workflow, including data from various nucleic acids and LNP analyses
• Discover how Agilent instruments/technologies, such as the Fragment Analyzer and LC/MS systems, can be used for different CQAs
• Learn how Agilent is working together with its partners to provide reliable insights for all aspects of the IVT mRNA workflow

Who should attend?

• Researchers, lab managers, lab directors, QA/QC managers performing IVT mRNA analysis in biotherapeutics research and production

Certificate of attendance
All webinar participants can request a certificate of attendance, including a learning outcomes summary, for continuing education purposes.

For Research Use Only. Not for use in diagnostic procedures. PR7001-2498

Explore the various systems from Agilent Technologies including the Bioanalyzer, TapeStation, and Fragment Analyzer, that can address challenges in next-generation sequencing (NGS) quality control. Gain top tips on how you can improve your workflow and transform your NGS applications with reliable quality metrics.

Find best practices and guidance on how to analyze in vitro transcription messenger RNA (IVT mRNA) using the Fragment Analyzer from Agilent Technologies. Learn how various factors can affect the yield and quality such as mixing, denaturing and sample loading, to improve your analysis.

Discover Agilent’s automated electrophoresis solutions designed to help ensure experimental success through accurate sample quality assessment. With a focus on NGS and protein QC, these solutions offer flexible throughput and high-resolution performance to support and streamline your workflow.

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