Author of

• 18974

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  P3.02 - Biology/Pathology (ID 620)

  • Event: WCLC 2017
  • Type: Poster Session with Presenters Present
  • Track: Biology/Pathology
  • Presentations: 2
  • Moderators:
  • Coordinates: 10/18/2017, 09:30 - 16:00, Exhibit Hall (Hall B + C)

  • 24003

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    P3.02-055 - Detecting ALK, ROS1 and RET Gene Translocations in Non-Small Cell Lung Cancer (NSCLC) with the NanoString Platform (ID 9976)

    09:30 - 09:30  |  Author(s): M.L. Aguirre
    • Abstract
    • Slides

    Background:
    Identification of ALK, ROS1 and RET fusions is critical for guiding target therapy of lung cancers. In this study, we evaluated the transcript-based nanoString assay for detection of ALK fusions compared to immunohistochemistry (IHC) and FISH methods, and the simultaneous detection of ROS1 and RET transcripts in formalin-fixed and paraffin embedded tissues (FFPE).
    
    Method:
    A total of 44 patients with NSCLC were selected for this non-consecutive case study. Samples included 24 cases of non-smokers or patients younger than 50 years with negative EGFR/ALK results that are more likely to contain a ROS1 or RET translocation. Eight cases with a discrepancy between ALK IHC and FISH results or equivocal IHC ALK results, as well as 12 cases previously confirmed positive for ALK by IHC were also included. The specimens were assessed for ALK, ROS1 and RET fusion transcripts by nanoString nCounter profiling.
    
    Result:
    While nanoString demonstrated 94.9% concordance with IHC and 84.2% concordance with FISH, it detected unknown ALK active transcripts in 3 of 7 cases that showed a discrepancy between IHC and FISH, or which were negative for ALK by IHC and FISH (see table 1). The three equivocal ALK IHC cases were scored negative by the 2 other methods. In addition to ALK, 3 cases of ROS1 and 2 cases of RET fusions were detected by nanoString. ALK, ROS1 and RET fusions were found mutually exclusive. Table 1. Discrepancy of ALK findings by IHC, FISH and nanoString, and crizotinib response

    Case	IHC	FISH	FISH positive nuclei (%)		nanoString		Crizotinib response
    1	Positive	Negative	3.9		Unknown ALK active fusion		Positive
    2	Negative	Negative	3.3		Unknown ALK active fusion		Positive
    3	Negative	Negative	8.6		Unknown ALK active fusion		Unknown
    4	Negative	Borderline	17.3		Negative		Not treated
    5	Negative	Borderline	15.1		Negative		Not treated
    6	Negative	Borderline	19.7		Negative		Not treated
    7	Negative	Positive	24		Inconclusive		Unknown

    
    
    Conclusion:
    NanoString performed well in lung cancer FFPE tissue including cytology materials. The results are highly concordant with the current standard methods of ALK-1 IHC and FISH. As a single test, it detected ALK, ROS1 and RET fusions simultaneously. NanoString profiling can be an alternative for a one tube test for ALK, ROS1 and RET translocations in a selected NSCLC patient group.
    
    

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  • 24588

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    P3.02-097c - Detection of the EGFR P.(T790M) Mutation by Different Methods: A Small Comparison Case Study (ID 10260)

    09:30 - 09:30  |  Author(s): M.L. Aguirre
    • Abstract

    Background:
    About 50-60% of non-small cell lung cancer (NSCLC) patients with a Tyrosine Kinase Inhibitor (TKI) sensitizing EGFR mutation can develop therapy resistance via the acquisition of the additional p.(T790M) mutation. The identification of this group of patients is important because they can be treated with a 3[rd] line TKI: Osimertinib. Analysis of plasma samples has become a minimally invasive alternative to repeat tissue biopsy for the detection of the EGFR p.(T790M) mutation. The mutation can be detected in plasma and tissue by various methods including the FDA approved Roche COBAS® EGFR v2 test, the EntroGen® EGFR test and digital droplet PCR (ddPCR). In this study, we compared the detection of the EGFR p.(T790M) mutation by ddPCR and COBAS in plasma specimens, and ddPCR and EntroGen in tissue specimens.
    
    Method:
    Blood from 14 NSCLC was collected in STRECK™ blood collection tubes. Plasma was prepared and circulating cell-free (ccf) DNA extracted with the COBAS and Qiagen method. DNA was analyzed for the presence of the EGFR TKI sensitizing and p.(T790M) mutation by COBAS, or the p.(T790M) mutation only by ddPCR on a Biorad QX200 platform. In addition, 26 biopsies from EGFR-positive patients who progressed on TKI, and which were tested p.(T790M) negative by Entrogen were re-analyzed by ddPCR.
    
    Result:
    Nine out of fourteen plasma samples were found to contain DNA with the sensitizing EGFR mutation by COBAS. The p.(T790M) mutation was found in four of these nine cases. ddPCR revealed one additional p.(T790M)-positive plasma sample that was tested negative by COBAS. ddPCR detected ten p.(T790M)-positive cases in the 26 EntroGen p.(T790M) negative samples, and suggests a 38% of false negative rate of the EntroGen method in this small cohort of samples.
    
    Conclusion:
    ddPCR for the detection of the EGFR p.(T790M) mutation in plasma and tissue appears to be associated with a higher sensitivity compared to the COBAS and EntroGen methods, respectively.