Cancer somatic mutation profiling is becoming an integral part of cancer management due to a pressing need to identify driver mutations to guide targeted therapy. An ideal detection assay covers all known clinical actionable mutations, require limited DNA, identify mutations accurately and be cost effective. We developed and validated a multigene analysis assay using DNA mass spectrometry covering the majority of currently clinically actionable mutations, particularly those in EGFR, KRAS, NRAS, BRAF and KIT. In comparison with the same coverage of single gene tests with sequential analysis, the mass spectrometry assay is fast (amplification, extension and MADL-TOF analysis for 8-64 samples in two days) and cost-effective. The concordance rate was over 98% between the mass spectrometry assay and Sanger sequencing, with a detection limit of 5-10% of the variant allele.
In diagnostic samples we identified driver mutations in 46%, 48% and 61% for 1110 melanomas, 554 non-small cell carcinomas and 211 colorectal cancers, respectively. In melanoma BRAF mutations were the commonest detected in 23% of patients (57% were V600E, 26% V600K and 17% exon 11 mutations), followed by NRAS (18.2%) and KIT mutations (1.8%). In lung adenocarcinoma EGFR mutations were detected in 21.7% of patients, KRAS in 21.3% and BRAF in 2.7% with rarer mutations detected in PIK3CA, PDGFR and ERBB2.
There was a very low assay failure rate (1.4%) and the average turnaround time was 5-10 days from receipt of the sample in the laboratory. Our results show that the mass spectrometry assay is fast and accurate in the cancer somatic mutation analysis and provides interesting insights into patterns of driver mutations in Australian patients in a routine diagnostic setting. A high mutation detection rate maximises opportunities for patients to receive personalised therapy.