MAY 07, 2020 7:00 AM PDT

A complete workflow for analysis of cfDNA: from plasma to variants

Sponsored by: Beckman Coulter, IDT
C.E. Credits: P.A.C.E. CE Florida CE
Speakers
  • Senior Applications Scientist in Automation & Biotechnology Business Unit at Beckman Coulter Life Sciences
    Biography
      Shilpa Parakh, is a Senior Applications Scientist in Automation & Biotechnology Business Unit at Beckman Coulter Life Sciences. Her focus is on automating genomics workflows on Biomek and Echo liquid handling platforms. Her past experiences include working in the Biomolecular Screening and Drug Discovery side where she was involved in developing, optimizing and running biochemical and cell-based assays on various liquid handling systems. Shilpa holds a Master's in Biotechnology from Western Michigan University.
    • Research Scientist, IDT
      Biography
        Nicole Roseman obtained her M.S. from Western Illinois University. Her research focused on studying polyploidy of Hyla versicolor from Hyla chrysoscelis using microstatellite analysis. Before graduating, she started at Integrated DNA Technologies as an intern in Biophysics learning target capture and testing modifications of oligonucleotides to normalize melting temperature and duplex stability. Now, Nicole works as a Research Scientist focusing in target capture and automation in Product Development's Verification and Validation department.

      Abstract

      DATE: May 7, 2020

      TIME: 7:00am PT

       

      As cost of sequencing continues to drop, the throughput and complexity of NGS assays have risen precipitously. At the same time, the types of samples being used for these assays have expanded as researchers find value in studying low input, degraded biological samples, such as cell free DNA (cfDNA). Obtaining actionable information from clinical samples is challenging due to loss during extraction, low conversion during NGS library preparation, drop in complexity during target enrichment, and sequencing and PCR errors that lead to low limits of detection. Here, we present a complete workflow for effective analysis of <1% AF variants in cfDNA. Our magnetic bead-based extraction kit provides complex, high yield recovery of cfDNA. A novel library prep chemistry delivers higher complexity and coverage than conventional TA ligation-based workflows, enabling highly sensitive low-frequency variant detection. In addition, fixed unique molecular index (UMI) sequences aid strand-specific molecular indexing by independently tagging the top and bottom strands, and can be used for various deduplication and error correction strategies. Our target enrichment strategies maintain high library diversity and on-target rates to enable low frequency variant calling regardless of panel size. We pair these chemistries with modularly designed automation protocols which provide users with safe stopping points, enabling customizable, high throughput solutions. By combining a high conversion extraction and library preparation chemistry with efficient hybridization capture, we demonstrate an effective approach to extract information from low quantity challenging samples.

       

      Learning Objectives:

      • Describe how to increase cfDNA extraction efficiency using magnetic bead–based technology.
      • Demonstrate how to maximize conversion, coverage and complexity from low inputs of cfDNA during library preparation.
      • Utilize fixed UMIs for bioinformatic error correction to reduce sequencing and PCR errors.
      • Discuss how to increase throughput, reduce hands-on time, and minimize errors during complex NGS assays.

       

      Webinars will be available for unlimited on-demand viewing after live event.

       

      LabRoots is approved as a provider of continuing education programs in the clinical laboratory sciences by the ASCLS P.A.C.E. ® Program. By attending this webinar, you can earn 1 Continuing Education credit once you have viewed the webinar in its entirety.  CE credits are available for this webinar up to 2 years from the date of the live broadcast.


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