Comparison of MET gene amplification analysis by next-generation sequencing and fluorescence in situ hybridization

Christina Schmitt; Anna-Alice Schulz; Ria Winkelmann; Kevin Smith; Peter J Wild; Melanie Demes

doi:10.18632/oncotarget.28092

Comparison of MET gene amplification analysis by next-generation sequencing and fluorescence in situ hybridization

Oncotarget. 2021 Oct 26;12(22):2273-2282. doi: 10.18632/oncotarget.28092.

Authors

Christina Schmitt¹, Anna-Alice Schulz¹, Ria Winkelmann¹, Kevin Smith¹, Peter J Wild^{1

2

3}, Melanie Demes^{1

2}

Affiliations

¹ Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany.
² Wildlab, University Hospital Frankfurt MVZ GmbH, Frankfurt am Main 60590, Germany.
³ Frankfurt Institute for Advanced Studies (FIAS), Frankfurt am Main 60438, Germany.

Abstract

MET gene alterations are known to be involved in acquired resistance to epidermal growth factor receptor inhibition. MET amplifications present a potential therapeutic target in non-small cell lung cancer. Although next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) are conventionally used to assess MET amplifications, there are currently no clinically defined cut-off values for NGS, with FISH still being the gold standard. A collective of 20 formalin-fixed paraffin-embedded lung cancer tissue samples (mean age 64 years) were selected based on increased MET gene copy number (CNV) status or the presence of mutations detected by NGS (GeneReader, QIAGEN) and were further assessed by FISH (MET/CEN7, Zytomed). Of these, 17 tumor samples were MET-amplified and one patient was found to have a MET rearrangement by NGS, while two samples had no MET gene alteration. In contrast to the NGS result, FISH analysis showed only one highly amplified sample and 19 negative samples. The single highly amplified case detected by FISH was also positive by NGS with a fold change (FC) of 3.18 and a mean copy number (CN_{MV 10-100%}) of 20.5. Therefore, for the assessment of MET amplifications using the QIAGEN NGS workflow, we suggest detecting amplified cases with an FC value of ≥ 3.0 and a CN_{MV 10-100%} value of ≥ 20.0 by FISH. In summary, NGS allows for DNA- and RNA-based analysis of specific MET gene amplifications, point mutations or rearrangements.

Keywords: MET amplification; fluorescence in situ hybridization (FISH); next-generation sequencing (NGS); non-small cell lung cancer (NSCLC); routine diagnostics.