Comparison of gene amplification analysis by next-generation sequencing and fluorescence hybridization.

gene alterations are known to be involved in acquired resistance to epidermal growth factor receptor inhibition. amplifications present a potential therapeutic target in non-small cell lung cancer. Although next-generation sequencing (NGS) and fluorescence hybridization (FISH) are conventionally used to assess 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 gene copy number (CNV) status or the presence of mutations detected by NGS (GeneReader, QIAGEN) and were further assessed by FISH (/CEN7, Zytomed). Of these, 17 tumor samples were -amplified and one patient was found to have a rearrangement by NGS, while two samples had no 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) of 20.5. Therefore, for the assessment of amplifications using the QIAGEN NGS workflow, we suggest detecting amplified cases with an FC value of ≥ 3.0 and a CN value of ≥ 20.0 by FISH. In summary, NGS allows for DNA- and RNA-based analysis of specific gene amplifications, point mutations or rearrangements.