Molecular markers


Resident / Fellow Advisory Board: David B. Chapel, M.D.
Deputy Editor-in-Chief: Patricia Tsang, M.D., M.B.A.
Bart Koopman, M.D., Ph.D.
Léon C. van Kempen, Ph.D.

Last author update: 18 November 2021
Last staff update: 18 November 2021

Copyright: 2021,, Inc.

PubMed Search: Molecular markers MET[TI] review[PT]

Bart Koopman, M.D., Ph.D.
Léon C. van Kempen, Ph.D.
Page views in 2022: 635
Page views in 2023 to date: 313
Cite this page: Koopman B, van Kempen LC. MET. website. Accessed June 2nd, 2023.
Definition / general
Essential features
Diagrams / tables

Images hosted on other servers:
Exon 14 skipping mutations

Exon 14 skipping mutations

Clinical features
Uses by pathologists
  • MET IHC correlates poorly with amplifications and exon 14 skipping and therefore has no practical use for pathologists (J Thorac Oncol 2019;14:1666)
  • NGS or FISH testing for acquired MET amplification can identify EGFR mutant or ALK rearranged patients who may benefit from second line dual EGFR / MET or ALK / MET inhibition (Lancet Oncol 2020;21:373, Clin Cancer Res 2020;26:2535)
  • Multiplex RNA sequencing or NGS can detect exon 14 skipping in NSCLC patients who may benefit from MET inhibitors
Prognostic factors
Molecular / cytogenetics description
  • Fluorescence in situ hybridization
  • Next generation sequencing (NGS)
    • Limited sensitivity / specificity to detect amplification; suspected copy number gain requires FISH confirmation (Nat Rev Clin Oncol 2020;17:569, BMC Cancer 2020;20:291)
    • Unbiased detection of MET exon 14 skipping mutations
    • Coverage required of the splice acceptor site, donor site and intronic regions adjacent to the splice acceptor (Cancer Discov 2015;5:850)
    • Highly variable mechanisms which may include substitutions, insertions, deletions and frameshift mutations (JCO Precis Oncol 2021;5:PO.20.00516, Histopathology 2021;78:1043)
    • Detection of a confirmed exon 14 skipping inducing DNA mutation may not require confirmation at RNA level
    • Detection of an unknown mutation affecting the exon 14 skipping hotspot regions should prompt an RNA based confirmation test
  • RNA analysis
    • Enables directly confirming the expression of an exon 13 - exon 15 fused mRNA transcript or MET fusions
    • Available techniques include anchored multiplex PCR (Invitae Archer® FusionPlex), targeted RNA sequencing (Asuragen QuantideX®) and molecular counting using fluorescent probes (NanoString nCounter®), among others (J Thorac Oncol 2019;14:737, J Mol Diagn 2019;21:352, Mol Oncol 2021;15:350)
    • Multiplex RNA sequencing techniques allow concurrent detection of MET exon 14 skipping, as well as (potentially) actionable fusions involving ALK, BRAF, FGFR1, FGFR2, FGFR3, MET, NRG1, NTRK1, NTRK2, NTRK3, RET and ROS1 in NSCLC
Molecular / cytogenetics images

Contributed by Léon C. van Kempen, Ph.D.
Normal MET

Normal MET

MET polysomy

MET polysomy

MET amplification MET amplification

MET amplification

Sample pathology report
  • Stage IV NSCLC with EGFR c.2236_2250del p.(E746_A750del) mutation
  • Patient presenting with progressive disease during treatment with an EGFR inhibitor
  • Biopsy: metastases in the soft tissue of the os ilium
  • Requested: mutation analysis to identify mechanism of resistance and options for targeted therapy
  • Result of DNA mutation analysis via next generation sequencing:
    • Percentage of tumor cells in the biopsy for DNA extraction: 30%
    • Two mutations detected: EGFR (NM_005228.3): c.2236_2250del p.(E746_A750del), 27% variant allele frequency and MET (NM_000245.4): c.2888-44_2899delinsA p.(?), 33% variant allele frequency
    • No indication of MET amplification
  • Result of RNA analysis to confirm MET exon 14 skipping
    • Percentage of tumor cells in the biopsy for RNA extraction: 30%
    • MET exon 14 skipping transcripts detected
  • Result of DNA FISH analyses to detect MET amplification
    • Area for FISH analysis indicated by the pathologist
    • Number of MET copies per cell: 1.5
    • MET/CEP7 ratio: 0.8
    • No amplification of MET
  • Conclusion: In addition to the EGFR exon 19 deletion mutation, a MET exon 14 skipping mutation and transcript was detected in this biopsy. In general, patients with this combination of mutations respond to treatment with dual inhibition of EGFR and MET.
  • Methodology: Selection of area containing neoplastic cells and estimation of percentage of neoplastic cells in that region was performed by a pathologist. DNA extraction from formalin fixed and paraffin embedded tissue was performed with the Maxwell CSC system (CE-IVD, Promega). Next generation sequencing was performed with the TSO500 panel (Illumina) on a NextSeq platform (Illumina). A > 100 unique coverage of > 98% of all coding regions is required for the detection of a 5% variant allele frequency with more than 95% confidence in tissue with at least 20% neoplastic cells. These quality criteria were met unless stated otherwise. Interpretation of pathogenicity and actionability was according to ACMG and AMP guidelines (J Mol Diagn 2017;19:4, Genet Med 2015;17:405). RNA was extracted with the Maxwell CSC system. RNA sequencing was performed using Archer Fusionplex (SK0133, Invitae) on a MiSeq system (Illumina). Data was analyzed with the Archer analysis tool 6.2. MET FISH analysis on FFPE tissue was performed with the MET (Vysis MET SpectrumRed FISH Probe [06N05-020] and the Vysis CEP 7 [D7Z1] SpectrumGreen Probe [06J37-007]) and counterstained with DAPI. FISH signals were counted in at least 50 neoplastic cells in by 2 independent observers. The laboratory is regulated under NEN-EN-ISO15189 as qualified to perform high complexity testing.
Board review style question #1
A 63 year old man presents with primary adenocarcinoma of the lung with radiological imaging suggestive of metastases to the bones, liver and lymph nodes. Molecular analysis of a lung biopsy (with 60% tumor cells) using next generation sequencing shows no mutations in EGFR, KRAS or BRAF. However, a splice site mutation is detected in MET [NM_000245.4]: c. 2888-30_2898del p.(?) with 42% variant allele frequency. To our knowledge, this specific variant has not been previously described. What is your next step?

  1. No additional test; report the detected mutation in the pathology report
  2. Perform an RNA analysis
  3. Perform fluorescent in situ hybridization (FISH)
  4. Perform MET immunohistochemistry
  5. Recommend treatment with a MET inhibitor
Board review style answer #1
B. Perform an RNA analysis. This is a deletion mutation within the splice site region of MET intron 13 - exon 14. However, this is not a previously described MET exon 14 skipping inducing mutation. Therefore, confirmation of the expression of an exon 13 - exon 15 fused mRNA transcript is necessary. This can be done using an RNA based analysis.

Comment Here

Reference: MET
Back to top
Image 01 Image 02