Comparison of two techniques used in screening non-small cell lung cancer (NSCLC) tumour samples demonstrated that fragment analysis could detect large MET exon 14 skipping deletions that were missed by next-generation sequencing (NGS), according to findings presented at the MAP 2020 Virtual Congress.
Lead author Romain Loyaux and colleagues from the Molecular Oncology Department, Hopital Europeen Georges-Pompidou – APHP in Paris, France conducted this study to evaluate the utility of NGS compared with fragment analysis for the detection of MET exon 14 alterations, including skipping deletions that act as an oncogenic driver and are observed in 1 to 4% of NSCLC tumours.
Capmatinib (Tabrecta, Novartis) was recently approved by the US Food and Drug Administration for management of adult patients with metastatic NSCLC with MET exon 14 skipping mutations, making detection of MET alterations needed to identify candidates for the treatment with capmatinib.
In addition, MET exon 14 mutations may serve as a marker of low response rates to treatment with immune checkpoint inhibitor therapy, despite high tumour PD-L1 expression.
NGS failed to detect two large MET exon 14 skipping deletions and may provide false negative results
The investigators examined 87 NSCLC wild-type samples for MET exon 14 by NGS and fragment analysis that were obtained in routine settings within an 18-month period from patients with driver wild-type NSCLC.
MET exon 14 skipping was screened by fragment analysis to detect large deletions in MET exon 14 and by DNA NGS on a Ion Proton plateform using ampliseq technology. Large deletions detected by only fragment analysis were also characteriesed by Sanger sequencing. PD-L1 tumour expression was quantified by immunohistochemistry.
Of the 87 patient samples evaluated by fragment analysis and sequencing, a MET exon 14 skipping alteration was detected in 13 patients. Among the 13 patients, eight samples had deletion impacting splice site and five had splice variants. Among the eight deletions, two were large deletions of 41 bp and 66 bp. These two deletions were only determined by fragment analysis and were not detected by NGS.
Histologically, there was no enrichment in samples with sarcomatoid features.
However, an association with PD-L1 expression was observed; samples with MET exon 14 skipping presented higher values of PD-L1 than other tumours screened in this study.
Detection of MET alterations is warranted for first-line treatment decision to detect exon 14 skipping and allow patient access to targeted therapy, such as capmatinib, as well as to identify patients that may have a poor response to immunotherapy, according to the authors. They concluded that these results highlight the limit of NGS to analyse large deletions and the risk of false negative results.
This study underscores that NGS, using standard pipelines and panels, may fail to detect MET exon 14 mutations. Association of complementary methods or large coverage intron screening could be alternatively used in order not to miss samples with MET alterations that could impair first-line treatment choices in patients with NSCLC.
The link between MET exon 14 and PD-L1 expression warrants further study.
No external funding was disclosed for this study.
Prof. Albrecht Stenzinger of the Institute of Pathology, University Hospital of Heidelberg in Heidelberg, Germany who discussed the study findings said that it is an important proof of concept study. It is elegant and quick way to identify large deletions, particularly for ampliseq sequencing; in general, you can make sure that flanking regions are well covered by DNA assay; and combining DNA and RNA sequencing for MET exon 14 skipping is critical.
4MO – Loyaux R, Blons H, Garinet S, et al. MET exon 14 screening strategy, how not to miss large deletions. MAP 2020 Virtual Congress (9-10 October 2020).