Table 1.

Detection techniques for MET aberrations.

MET Aberration	Detection Technique	Tested Material	Evaluation Criteria	Advantages	Disadvantages
MET overexpression [14,15,16,17,18,19,20,21,22,23]	IHC antibodies	FFPE slide	Semi-quantitative score 0–3+	Technique widely used and available, fast and cheap	Observer-dependent, tissue sectioning artefacts, new FFPE slide for every analysis, no consensus on scoring system and cutoff
MET exon 14 skipping [25,26,27,28,29,30,31,32,33,34,35,36,37,38,39]	RNA NGS (amplicon-, AMP-, or hybridization-based)	RNA from FFPE or fresh frozen material	Mutation, coverage, MAF, fusion product of exon 13 and 15	Sensitive, reliable, direct detection of alternative splicing, multiplexing	RNA degradation, underlying mutation cannot be determined
	RT-PCR	RNA from FFPE or fresh frozen material	Fusion product of exon 13 and 15	Sensitive, reliable, direct detection of alternative splicing, fast turnaround time, widely used and available	RNA degradation, underlying mutation cannot be determined, targeted mutations only
MET exon 14 skipping mutations and point mutations [33,35,37,40,41,42,43,44]	DNA NGS (amplicon- or hybridization-based)	DNA from FFPE, fresh frozen material, or liquid biopsy	Mutation, coverage, VAF	Sensitive, reliable, detection of exact mutation, multiplexing	No assessment of splicing effect
	Sanger sequencing	DNA from FFPE, fresh frozen material, or liquid biopsy	Mutation, VAF	Detection of exact mutation, fast turnaround time, widely used and available	Sensitivity, single assay for each target, no assessment of splicing effect
MET amplifications [5,41,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61]	FISH	FFPE slides	MET GCN, MET/CEN7 ratio	Technique widely used and available, detection of focal amplification, polysomy, and chromosome duplications	Observer-dependent, tissue sectioning artefacts, new FFPE slide for every analysis, no consensus on scoring system and cutoff
	DNA NGS (amplicon- or hybridization-based)	DNA from FFPE, fresh frozen material, or liquid biopsy	Mutation, coverage, VAF	Sensitive, DNA from FFPE easily accessible, multiplexing	High number of false negatives, no standardized cutoff or bioinformatics, no morphological correlation
	Other DNA-based technologies (ddPCR, NanoString nCounter technology)	DNA from FFPE, fresh frozen material, or liquid biopsy	Expression, GCN	DNA from FFPE easily accessible	High number of false negatives, no morphological correlation, no standardized cutoff, large amounts of DNA needed
MET fusions [35,39,62,63,64,65,66,67,68,69,70,71]	RNA NGS (AMP- or hybridization-based)	RNA from FFPE or fresh frozen material	Fusionreads, 3′-5′ imbalance	Sensitive, reliable detection of known and novel fusion partners, multiplexing	RNA degradation
	DNA NGS (Hybridization-based)	DNA from FFPE	Fusionreads, 3′-5′ imbalance, coverage,	DNA from FFPE easily accessible, detection of known and novel fusion partners if region is covered, multiplexing	False negative results, novel fusions are problematic due to location of fusion break point
	FISH	FFPE slides	n.a. break-apart events	Technique widely used and available	No standardized assay available, observer-dependent, tissue sectioning artefacts, new FFPE slide for every analysis
	RT-PCR	RNA from FFPE	Fusion product	Technique widely used and available	No standardized assay available, only for known fusion partners, RNA degradation

IHC: immunohistochemistry; FISH: fluorescence in situ hybridization; FFPE: formalin-fixed paraffin-embedded; RT-PCR: quantitative real-time polymerase chain reaction; ddPCR: digital droplet PCR; n.a.: not available; GCN: gene copy number; CEN7: centromere of chromosome 7; AMP: anchored multiplex polymerase chain reaction; NGS: next-generation sequencing; VAF: variant allele frequency.