Abstract
Molecular diagnostics in cancer pharmacogenomics is indispensable for making targeted therapy decisions especially in lung cancer. For routine clinical practice, the flexible testing platform and implemented quality system are important for failure rate and turnaround time (TAT) reduction. We established and validated the multiplex EGFR testing by MALDI-TOF MS according to ISO15189 regulation and CLIA recommendation in Taiwan. Totally 8,147 cases from Aug-2011 to Jul-2015 were assayed and statistical characteristics were reported. The intra-run precision of EGFR mutation frequency was CV 2.15% (L858R) and 2.77% (T790M); the inter-run precision was CV 3.50% (L858R) and 2.84% (T790M). Accuracy tests by consensus reference biomaterials showed 100% consistence with datasheet (public database). Both analytical sensitivity and specificity were 100% while taking Sanger sequencing as the gold-standard method for comparison. EGFR mutation frequency of peripheral blood mononuclear cell for reference range determination was 0.002 ± 0.016% (95% CI: 0.000–0.036) (L858R) and 0.292 ± 0.289% (95% CI: 0.000–0.871) (T790M). The average TAT was 4.5 working days and the failure rate was less than 0.1%. In conclusion, this study provides a comprehensive report of lung cancer EGFR mutation detection from platform establishment, method validation to clinical routine practice. It may be a reference model for molecular diagnostics in cancer pharmacogenomics.
Highlights
The identification of these driver mutations is necessary for the treatment decision
We focused on the quality issues including method validation, procedure, turnaround time and statistical characteristics
After inactivation of dNTP by shrimp alkaline phosphatase (SAP) treatment, the single nucleotide extension reaction was performed by the specific probe annealed to one nucleotide before the mutation site
Summary
The identification of these driver mutations is necessary for the treatment decision. Kris et al showed that patients with driver mutations who received the corresponding drugs had a prolonged progress-free survival than those with a driver mutation who did not receive the drugs and those without driver mutations[9] This suggested that the companion molecular diagnostics-guided therapy is the trend in cancer management to improve patients’ survival[10]. Even the issue of well characterized quality assurance has come to a consensus, the guideline or the regulation is still debated This was because of a lot of high-sensitive and high throughput platforms were developed and the difficulties in method validation needed to be solved. We focused on the quality issues including method validation, procedure, turnaround time and statistical characteristics This can be a reference for cancer molecular diagnostics
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