Detecting EGFR mutations (L858R, T790M) using allele specific multiplex sequencing: A comparison with Pyrosequencing and TruSeq

Abstract

We are presenting an evaluation of Allele Specific Multiplex Sequencing (ASMS) to detect two EGFR somatic mutations (L858R, T790M). Late stage lung cancer samples were tested for both EGFR mutations and were compared to either pyrosequencing or TruSeq. The analytical lower limit of detection (LLOD) for the ASMS-L858R assay was found to be 36 copies, and 72 copies for the ASMS-T790M assay. The forty-one FFPE samples that were tested for T790M showed 100% concordance with the respective comparative method. The forty-five FFPE samples tested previously by Truseq for L858R showed 100% concordance with ASMS. Out of the twenty L858R samples previously tested by pyrosequencing, there was 95% concordance with ASMS. Additionally, twenty-one normal blood samples were tested by ASMS were found to be negative for L858R and T790M. In conclusion, the detection of L858R and T790M by ASMS are in acceptable concordance with both pyrosequencing and TruSeq in detecting EGFR mutations from late stage lung cancer. Further, ASMS was able to detect EGFR (L858R) with 10 picograms (3 copies gDNA) of FFPE extracted DNA, and hence could be used to detect mutations from samples carrying low copy numbers.