Abstract 1211: High throughput somatic mutation profiling in non-small cell lung adenocarcinoma using MALDI-TOF Mass spectrometry.
Authors: Antoinette Lemoine, Raphael Saffroy, Nelly Bosselut, Jean-Francois Morere, Aleksey Nakorchevsky, Dirk van den Boom, Mathias Ehrich, Darryl Irwin, Anders Nygren
Journal: Cancer Research (2013)

Abstract In the current era of genomics, lung cancer research has made great strides in dissecting the molecular basis of individual tumors. As more mutations are identified, it is clear that the research community needs to interrogate multiple genes to generate an accurate molecular profile for each individual tumor. Molecular classification of large sample sets requires a flexible high-throughput solution that can easily adapt to newly discovered mutations as well as detect minority alleles of mutated DNA. Validation of key mutations requires screening against thousands of samples with a more directed, high-throughput technique such as MALDI-TOF mass spectrometry (MassARRAY® system). We have evaluated the LungCarta™ Panel, a panel targeting 213 somatic mutations in 26 genes frequently mutated in Non-Small Cell Lung Adenocarcinoma (NSCLC). The method relies on multiplex PCR followed by single base extension and analysis using MALDI-TOF Mass Spectrometry. This panel was designed from a candidate pool of more than 1000 mutations identified in the large scale sequencing study with further selection and priority given to mutations that may be implicated in key pathways or of interest for clinical research. Frequently mutated genes such as EGFR, KRAS, BRAF and NRAS are well-represented and newly identified genes were included for further confirmation against larger sample numbers including MAP2K1, EPHA3, NTRKs, STK11, TP53 and DDR2. For verification of this panel we have screened a set of 37 lung tumor DNA samples isolated from formalin fixed paraffin embedded (FFPE) NSCL Adenocarcinomas. These samples were previously characterized for EGFR, KRAS, ERBB2, PIK3CA and BRAF. We identified mutations in 23 samples (62%) localized in 10 genes including 9 novel mutations and all of the 13 previously known mutations were verified. Interestingly, four of the samples contained more than one mutation with two samples carrying 2 separate mutations in the EGFR gene. In addition, by performing a quality test of the FFPE DNA we were able to significantly reduce the DNA amount used for testing, a necessity as the amount of DNA obtained from NSCLC FFPE sample is low. In conclusion, we show that MALDI-TOF mass spectrometry is an ideal tool for high-throughput screening of these types of genetic lesions in NSCLC. The LungCarta Panel provides a targeted, mid-density research panel for cost-effective and rapid analysis. Key somatic mutations in previously annotated genes and pathways can be rapidly confirmed against larger sample numbers. The discovery and confirmation of mutation profiles by tumor subtype will supplement other clinical research observations such as histology and grade to uncover new directions in translational and clinical research on NSCLC. Citation Format: Antoinette Lemoine, Raphael Saffroy, Nelly Bosselut, Jean-Francois Morere, Aleksey Nakorchevsky, Dirk van den Boom, Mathias Ehrich, Darryl Irwin, Anders Nygren. High throughput somatic mutation profiling in non-small cell lung adenocarcinoma using MALDI-TOF Mass spectrometry. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1211. doi:10.1158/1538-7445.AM2013-1211