Author of

• 17629

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  P2.03b - Poster Session with Presenters Present (ID 465)

  • Event: WCLC 2016
  • Type: Poster Presenters Present
  • Track: Advanced NSCLC
  • Presentations: 1
  • Moderators:
  • Coordinates: 12/06/2016, 14:30 - 15:45, Hall B (Poster Area)

  • 17727

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    P2.03b-098 - Comparison of Digital PCR, Ion Proton with ARMS-PCR in Tumor Tissue and Plasma of NSCLC Patients (ID 5544)

    14:30 - 14:30  |  Author(s): X. Li
    • Abstract

    Background:
    Deletions in exon 19 and heterozygous mutations (e.g. L858R) in exon 21 are the mutation hotspots of EGFR mutations, which are validated to be sensitive to EGFR-TKI, while exon 20 T790M mutation of EGFR is resistant to EGFR-TKI. A biopsy is needed to characterize EGFR mutation status. However, the amplification-refractory mutation system PCR (ARMS-PCR) is limited to detect mutation frequency below 1%. The QuantStudio 3D Digital PCR (digital PCR) and NGS were new promising techniques for low frequency mutations detection. In current study, we identified the EGFR L858R, T790M and exon 19 Del using a customized Ion AmpliSeq panel and digital PCR, then compared the detection with ARMS-PCR. Besides, in need of liquid biopsy, we also assessed the consistence between tumor tissue and circulating DNA (ctDNA) in digital PCR platform.
    
    Methods:
    A total of 27 NSCLC patients with stage III/IV were enrolled, paired tumor tissue and plasma (within 7 days before/after tumor biopsy) were collected. ARMS-PCR were provided by hospital. DNA from tumor tissue was sequenced in Ion Proton system with a customized panel based on Ion Ampliseq Colon and Lung Cancer Research Panel and analyzed using digital PCR. The ctDNA was only detected in digital PCR. Mutation frequency was determined and analyzed to reveal the consistency of platforms or sample types.
    
    Results:
    Compared with ARMS-PCR identification in tumor tissues of 27 patients, all of the corresponding mutation status were identified in Ion Proton and digital PCR, while the specificity is 95.00% and 85.07% respectively. Compared with Ion Proton, digital PCR achieved 100% sensitivity and 89.06% specificity. Ion Proton identified two more T790M mutations, digital PCR identified other six T790M mutations and one L858R mutation with frequency between 0.1%-1%. For the tumor tissue mutations identified by Proton and digital PCR, the Spearman’s rank correlation coefficient showed a strong positive correlation (R[2]=0.9711). In digital PCR platform, plasma had 62.50% sensitivity, 100% specificity and 88.89% concordance with tumor tissue. However, the frequency called by plasma was lower than that of tumor tissue. Plasma in digital PCR had a sensitivity of 81.25%, specificity of 96.97% and total concordance of 93.95%.
    
    Conclusion:
    This study demonstrated comparable capacity of mutation detection using Proton and digital PCR compared with ARMS-PCR. Digital PCR could identify lower frequency mutations than Ion Proton. The ctDNA showed strong specificity detection in patients with NSCLC, while it also indicated that the lower frequency in tumor tissue, the less possibility to be detected in plasma.