Lung cancer mutation testing: a clinical retesting study of agreement between a real-time PCR and a mass spectrometry test

// Phillip Shepherd 1 , Karen L. Sheath 2 , Sandar Tin Tin 3 , Prashannata Khwaounjoo 4 , Phyu S. Aye 3 , Angie Li 4, 5 , George R. Laking 5 , Nicola J. Kingston 6 , Christopher A. Lewis 7 , J. Mark Elwood 3 , Donald R. Love 2 and Mark J. McKeage 4, 5 1 Auckland Uniservices, University of Auckland, Auckland 1142, New Zealand 2 Diagnostic Genetics, LabPlus, Auckland City Hospital, Auckland 1148, New Zealand 3 School of Population Health, University of Auckland, Auckland 1142, New Zealand 4 Pharmacology and Clinical Pharmacology and Auckland Cancer Society Research Centre, University of Auckland, Auckland 1142, New Zealand 5 Blood and Cancer Services, Auckland City Hospital, Auckland 1148, New Zealand 6 Anatomical Pathology, LabPlus, Auckland City Hospital, Auckland 1148, New Zealand 7 Respiratory Medicine, Auckland City Hospital, Auckland 1148, New Zealand Correspondence to: Mark J. McKeage, email: m.mckeage@auckland.ac.nz Keywords: agreement analysis; epidermal growth factor receptor; lung cancer; mutation testing; targeted therapy Received: July 23, 2017 Accepted: August 15, 2017 Published: September 16, 2017 ABSTRACT To investigate the clinical validity and utility of tests for detecting Epidermal Growth Factor Receptor ( EGFR ) gene mutations in non-squamous non-small cell lung cancer patients, tumour DNA extracts from 532 patients previously tested by the cobas EGFR Mutation Test (RT-PCR test) were retested by the Sequenom/Agena Biosciences MassArray OncoFocus mass spectrometry test (MS test). Valid results from both tests were available from 470 patients (88%) for agreement analysis. Survival data were obtained for 513 patients (96%) and 77 patients (14%) were treated with EGFR tyrosine kinase inhibitors (TKIs). Agreement analysis revealed moderately high positive (79.8%), negative (96.9%) and overall percentage agreement (93.2%) for the detection of EGFR mutations. However, EGFR mutations were detected by one test and not by the other test in 32 patients (7%). Retesting of discordant samples revealed false-positive and false-negative results generated by both tests. Despite this, treatment and survival outcomes correlated with the results of the RT-PCR and MS tests. In conclusion, this study provides evidence of the clinical validity and utility of the RT-PCR and MS tests for detection of EGFR mutations that predict prognosis and benefit from EGFR-TKI treatment. However, their false-positive and false-negative test results may have important clinical consequences.