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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
Tumour content ratio matters for detecting epidermal growth factor receptor mutation by cobas test in small biopsies;
Mariko Kogo1, Daichi Fujimoto2, Kazutaka Hosoya2
1Department of Respiratory Medicine, Kobe City Medical Center General Hospital, 2-1-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. m.k.kogo2@gmail.com.
Background:
Recent studies indicate the benefit of treatment with osimertinib over that with conventional epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) for untreated EGFR-mutated non-small cell lung cancer (NSCLC). Cobas ver2 is the only companion diagnostic method for detecting EGFR mutations with osimertinib treatment. We clinically experience false negative cases with this test, but its actual sensitivity is unknown. Moreover, no study has suggested the importance of tumour dissection, and most facilities do not routinely perform them on small biopsies. The purpose of this study was to evaluate the sensitivity of cobas in clinical practice and clarify the role of dissection as a component of the cobas testing.
Methods:
We examined 132 patients with EGFR-mutated NSCLC diagnosed by bronchoscopy and confirmed with PCR clamp. Patients were tested with cobas and the EGFR-positive rate was calculated. Samples with undetected EGFR mutations were retested after tumour dissection and the rate of samples whose EGFR mutation was corrected to positive was assessed. To evaluate tumour cellularity, the tumour content ratio was assessed by calculating tumour cell count over the total cell count on the slide.
Results:
The positive rate of EGFR mutation identification was 76% with cobas, although EGFR mutation-negative patients retained responses to TKI therapy equivalent to positive patients did; however, the tumour content ratio of negative samples was significantly lower than that of positive samples. Twenty-nine negative samples underwent dissection and 24% were corrected to positive. Moreover, 53% of the samples with a tumour content ratio below 10% was negative for cobas, but 33% of these turned positive after dissection.
Conclusions:
Cobas had a high false negative rate in clinical practice, and tumour content ratio might be associated with this rate. Dissection could improve the sensitivity of cobas, especially in samples with low tumour cellularity.
Insights
The Cobas test shows a high false negative rate for detecting EGFR mutations in non-small cell lung cancer. Tumor dissection can improve test sensitivity, especially for samples with low cellularity.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genetics
Background:
- Osimertinib offers benefits over traditional tyrosine kinase inhibitors (TKIs) for EGFR-mutated non-small cell lung cancer (NSCLC).
- Cobas ver2 is the sole companion diagnostic for detecting EGFR mutations for osimertinib treatment.
- Clinical observations suggest false negatives with Cobas, but its sensitivity is unquantified, and the role of tumor dissection is unexplored.
Purpose of the Study:
- To assess the clinical sensitivity of the Cobas EGFR mutation test.
- To determine the impact of tumor dissection on Cobas test accuracy in NSCLC.
Main Methods:
- Evaluated 132 NSCLC patients using Cobas testing.
- Retested samples negative for EGFR mutations after tumor dissection.
- Assessed tumor cellularity via tumor content ratio.
Main Results:
- Cobas identified EGFR mutations in 76% of cases.
- Tumor dissection corrected 24% of initially negative samples to positive.
- Samples with <10% tumor content showed higher false-negative rates, with 33% corrected post-dissection.
Conclusions:
- Cobas exhibits a significant false-negative rate in clinical practice.
- Low tumor cellularity is associated with Cobas test inaccuracies.
- Tumor dissection enhances Cobas sensitivity, particularly for samples with limited tumor cells.
