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

As the cost of sequencing continues to drop, the throughput and complexity of next generation (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 ultra-low-frequency 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. By combining the high conversion of our extraction and library preparation chemistry with our efficient hybridization capture technology, we demonstrate an effective approach to extracting information from low-quantity, challenging samples.

Learning objectives:

  • How to increase cfDNA extraction efficiency using magnetic bead-based technology
  • How to maximize conversion, coverage, and complexity from low inputs of cfDNA during library preparation
  • How to utilize fixed unique molecular identifiers (UMIs) for bioinformatic error correction to reduce sequencing and PCR errors
  • How to increase throughput, reduce hands-on time, and minimize errors during complex NGS assays

Presented by: 

  • Shilpa Parakh
    Senior Applications Scientist in Automation & Biotechnology Business Unit
    Beckman Coulter Life Sciences
  • Nicole Roseman
    Research Scientist
    Integrated DNA Technologies

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Event information


April 2-April 3, 2021