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Narumol Trachu



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    P2.01 - Advanced NSCLC (Not CME Accredited Session) (ID 950)

    • Event: WCLC 2018
    • Type: Poster Viewing in the Exhibit Hall
    • Track:
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/25/2018, 16:45 - 18:00, Exhibit Hall
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      P2.01-132 - Comparison Molecular Profiles in NSCLC by Using Different NGS Platforms and<br /> Different Variant Frequency Cutoff (ID 14349)

      16:45 - 18:00  |  Author(s): Narumol Trachu

      • Abstract
      • Slides

      Background

      There are several methods to detect molecular alterations in precision medicine era. This is a pilot study aimed to explore the concordance of molecular alterations testing using NGS different platforms and different cutoff allele frequency in NSCLC patients.

      a9ded1e5ce5d75814730bb4caaf49419 Method

      Ten NSCLC patients’ FFPE were retrieved for DNA extraction. All qualified samples were analyzed using NGS on 45 cancer genes panel on Ion Torrent system NGS Gene read Qiagen Lung Cancer Panel. Variants from NGS with coverage of are higher than 1000X. The cutoff 1% and 3% of variant allele frequency were considered positive. EGFR, BRAF, KRAS were validated by Real-time PCR technique using the Amoy DX and Actionable Insights Tumor Panel in GeneReader NGS system.

      4c3880bb027f159e801041b1021e88e8 Result

      We found 90%/30% EGFR-mutation, 40% BRAF V600E, 70%/30% KRAS-mutation by NGS using allele frequency cutoff at 1% and 3%, respectively. We validated by Real-Time PCR and Actionable GeneReader showed 70%/40% EGFR-mutation, 20%/10% BRAF V600E, and 0%/30% of KRAS-mutation (Table1). Regarding EGFR-mutation, 5 cases of discordance showed positive at 1% but negative at 3% cutoff allele frequency by NGS and validated by Real-Time showed positive all 5 cases. Two negative cases by Real-Time PCR show positive in NGS cutoff 1% (2/2) and 3% (1/2). In early stage (80%), there was 60% of EGFR 19 del detected by NGS cutoff 1%. The patients have continued follow-up at the clinic with the mDFS of 4.7 years. Two stage IV patients with exon19del were death and received EGFR-TKI as a second-line treatment with mOS at 1.1 and 1.2 years.

      Table 1

      Number of 10 cases positive

      NGS IonTorrent Cutt Off at 1%

      NGS Ion Torrent Cutt Off at 3%

      NGS GeneReader

      Real-time PCR

      EGFR Mutation

      9

      3

      4

      7

      Exon 19 Del

      6

      2

      2

      5

      L858R

      1

      0

      2

      2

      >1 EGFR Mutations

      2

      1

      0

      0

      No Mutation

      1

      7

      6

      3

      8eea62084ca7e541d918e823422bd82e Conclusion

      Different platform of NGS and different cutoff variant allele frequency gave the different result of gene frequency. We need to explore the standard of NGS testing including the proper cutoff for allele frequency in order to establish the most efficient method and correlate with the clinical treatment outcomes.

      6f8b794f3246b0c1e1780bb4d4d5dc53

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