Author of

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  P3.06 - Poster Session 3 - Prognostic and Predictive Biomarkers (ID 178)

  • Event: WCLC 2013
  • Type: Poster Session
  • Track: Biology
  • Presentations: 1
  • Moderators:
  • Coordinates: 10/30/2013, 09:30 - 16:30, Exhibit Hall, Ground Level

  • 12492

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    P3.06-052 - A novel technique that distinguishes low-level somatic DNA variants from FFPE-induced artifacts in lung and other solid tumors by next-generation sequencing (NGS) (ID 3502)

    09:30 - 09:30  |  Author(s): Q. Zhang
    • Abstract

    Background
    Next generation sequencing is a powerful tool to investigate somatic changes in tumor DNA. However the challenge is to detect low-frequency variants (< 10% minor allele frequency, MAF) in DNA extracted from formalin-fixed-paraffin-embedded (FFPE) tissue. DNA extracted from FFPE is highly fragmented and chemically modified. To overcome these challenges, we have developed a novel technique that can distinguish true variants from fixation artifacts with high sensitivity and specificity by investigating each of the two DNA strands independently.

    Methods
    TruSeq Custom Amplicon technology was used to generate sequencing libraries and deep sequencing was carried out to an average depth of 20,000X with a minimum of 1000X. The targeted re-sequencing assay* investigates ~14 kb of exons in 26 genes commonly mutated in solid tumors.

    Results
    Testing of more than 200 samples with a MAF ≥5%threshold revealed the presence of a large number of potentially false positive calls when data from only one strand of DNA was analyzed, but this number was significantly reduced (e.g. >50% for G>A) when both strands were considered.

    Conclusion
    This technique can distinguish FFPE artifacts from true variants and therefore provides increased accuracy for the detection of low-frequency variants by NGS. *Research Use Only