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Abstract: In this webinar, experts from Strata Oncology, will highlight the importance of cfDNA yield and purity using the Revolution Sample Prep System from nRichDx for cfDNA extraction as well as reliable pre-analytical quality control with the Agilent Cell-free DNA ScreenTape assay and the TapeStation systems, and their relation to NGS-based MRD testing.

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Abstract:This webinar will demonstrate how rigorous quality control (QC) of samples and libraries is crucial to produce high-quality data in next-generation sequencing (NGS). Sample QC metrics like concentration, DNA and RNA integrity numbers, 28S/18S ratio, DV200, fragment length, and amount of adapter dimers will be covered. How these metrics provide reasonable estimates for downstream NGS sequencing parameters such as on-target rate, duplication rate, and sequencing coverage will be discussed.

Speaker:Yves-Edouard Herpe, PhD, Manager, Biobanque de Picardie, France

Abstract:Bettina presents an overview about nucleic acid quality assessment with automated electrophoresis. Her talk exhibits the latest developments in nucleic acid sample quality control including application examples – from DNA to Cell-free DNA (cfDNA) - evaluated with different automated electrophoresis platforms like the TapeStation system and the Femto Pulse system.

Quality Control of Genomic DNA for the French Kidney Disease Study by the Biobanque de Picardie In his talk Dr. Herpe shares insights about The French Chronic Kidney Disease - Renal Epidemiology and Information Network (CKD-REIN) project - a large prospective cohort study that was established to identify the determinants, biomarkers, and practice patterns associated with chronic kidney disease outcomes. In this work Yves-Edouard shows that the Agilent 4200 TapeStation system with the Genomic DNA ScreenTape assay is a relevant QC tool to monitor the integrity of gDNA extracted from buffy coats stored frozen for up to five years.

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Abstract:Next-generation sequencing (NGS) is a fundamental tool in molecular biology laboratories, essential for routine and complex sample analysis. This webinar explores the benefits of sample quality control for two specific NGS challenges that researchers may encounter:

Part one investigates heteroduplex molecules or “daisy chains.” Most NGS workflows include an amplification step to increase adapter-ligated DNA available for sequencing. Optimizing the amplification cycle number helps minimize daisy chain artifacts, which can interfere with accurate library quantification. We will discuss how to identify ‘daisy chains’ and provide recommendations to avoid them.

Part two discusses the importance of assessing the final read length of NGS libraries prior to downstream analysis in order to avoid sequencing through the insert past the adapter. Sample quality assessment using automated electrophoresis enables researchers to confirm or adjust libraries for optimal insert length prior to NGS, helping to decrease background noise and improve quality scores of the sequencing run.

Speaker: Iraad Bronner, PhD Senior Staff Scientist of the Wellcome Sanger Institute DNA Sequencing facility

Abstract: Samples arriving to core facilities for genomic analysis can have diverse qualities profiles, presenting technical challenges for downstream applications such as next-generation sequencing (NGS). To help standardize sample processing and improve long-read NGS results, researchers at the Wellcome Sanger Institute have refined their high-molecular weight (HMW) DNA extraction protocols and implemented sample quality control (QC) testing. Iraad Bronner, PhD, Senior Staff Scientist of the Wellcome Sanger Institute’s DNA Sequencing facility, explains his systematic approach for optimal extraction of HMW DNA used for subsequent sequencing in this on-demand webinar. See the results of different extraction protocols, and explore how: The Agilent Femto Pulse system can be used for multiple library preparation steps Sample QC assists researchers in making informed decisions throughout the sequencing workflow

Speaker: Elisa Viering, M.Sc., Product Manager, Agilent and Monique Albert, Msc, Director Ontario Tumour Bank, Ontario Institute for Cancer Research

Abstract: It is widely assumed that the integrity of tissue specimens remains stable indefinitely if preserved at cryogenic temperatures. With biobanking reaching a level of maturity where samples are increasingly stored for 10 years and beyond, this assumption of prolonged stability should be tested. Data from such an assessment are critical to verify if samples stored for extended durations remain “fit for purpose” or if there is need to reconsider the utility of samples stored beyond a certain timeframe. The Ontario Tumour Bank has been collecting samples since 2004, and assesses a random selection of frozen samples each year for RNA and DNA integrity as a part of ongoing quality control (QC) practices.

Speaker: Steffi Sandke, Ph.D., Coordination Office and Scientific Management University Hospital Heidelberg, Heidelberg Cardiobiobank

Abstract: Retrospective analyses of DNA quality and quantity from samples collected over the last 9 years clearly showed that the implementation of SOPs and automated sample processing and storage systems lead to a significant improvement of sample quality and quantity. As the highest sample quality is needed for personalized and precision medicine, standardized processes are mandatory for Biobanks.

Speaker: Whitney Pike, MA, Application Scientist, Agilent Technologies

Abstract: Today the second part of the series will focus on QC during the library preparation process, from fragmentation to the final library for sequencing.

Speaker: Erin Bernberg, Ph.D., Senior Scientist, University Delaware

Abstract: In this PacBio User Group Meeting presentation, Erin Bernberg from the University of Delaware reports on using the Agilent Femto Pulse System for high-resolution, highly sensitive fragment analysis and on the low DNA input protocol, which her team used for a recent study of ice worms.