Methodology comparison and influence factors analysis of epidermal growth factor receptor mutation detection

Abstract

To compare two different methods in detecting epidermal growth factor receptor (EGFR) mutation status of non-small cell lung cancer (NSCLC) , and investing the influences of different conserving methods in DNA quantity, quality and detecting results of formalin-fixed paraffin embedded (FFPE) tissue samples. One hundred and fifty FFPE samples of advanced NSCLC were collected in Cancer Institute/Hospital, Chinese Academy of Medical Sciences from November 2010 to August 2011. Both scorpions amplification refractory mutation system (scorpions ARMS) and direct sequencing were used to detect EGFR mutation in exon 18, 19, 20 and 21, together analyzed the differences between these two methods. Samples with inconsistent results were collected clinical treatment and survival information for further analysis. Extracted DNA from 30 FFPE samples and conserved at -20 °C for 3 years, meanwhile the same 30 FFPE samples DNA were extracted after conserving for 3 years. The DNA quantity, quality and testing results of the two conserving methods were compared. The detection success rate of Scorpions ARMS (100%) was higher than direct sequencing (87.3%), with statistical significance ( χ(2) = 20.28, P < 0.05). The consistent rate of the two methods was 84.7%, and there were no significant differences between these two methods, with a high consistence (Kappa = 0.738, P < 0.001) . The clinical treatment and survival status of 5 patients with different testing results were analysed, which were consistent with ARMS testing results. The quality of DNA extracted from FFPE tissues which were conserved for 3 years according to the conventional way was worse and with more fragments compared with DNA conserved at -20 °C for 3 years, but the EGFR mutation detecting results of the DNA acquired from the two conserved ways were consistent. Combination of Scorpions ARMS and direct sequencing could make the detecting result more comprehensive and reliable. Clinical treatment and survival data may provide diagnosis support for cases with different mutation testing results. DNA extracted from FFPE samples and stored at low temperature is better for conserving the integrity.