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Table 3 RNA-based analysis of unequivocal ALK cases showed 100% concordance between digital probe-based assay and IHC and FISH results. ALK fusion detection based on 3′/5′ imbalance MPS assay showed 25% deviation for IHC-negative/FISH-negative cases and 33% deviation for IHC-positive/FISH-positive cases. Data showed 92% concordance between ALK fusion breakpoint detection by MPS assay and IHC and FISH for IHC-negative/FISH-negative samples and 100% accordance for IHC-positive/FISH-positive samples

From: RNA-based analysis of ALK fusions in non-small cell lung cancer cases showing IHC/FISH discordance

Sample IHC FISH Massive Parallel Sequencing (MPS) (IonTorrent) Probe-Based Assay (NanoString) Fusion
Fusion 3′/5’ Fusion 3′/5’
IHC-negative/FISH-negative
 P01 NA NA NA NA ND  
 P02 ±  
 P03 ±  
 P04  
 P05  
 P06 ND  
 P07 ND  
 P08 ND  
 P09 ND  
 P10 ND  
 P11 ND  
 P12 ND  
IHC-positive/FISH-positive
 P13 + + + + + + + V1
 P14 + + + ± + + V1
 P15 + + + + + + V3a/b
 P16 + + + + + + V2
 P17 + + + + ND V1
 P18 + + + + + + ND V6
  1. Fusion: fusion detection with amplicons/probes covering ALK fusion breakpoint; 3′/5′: fusion detection with amplicons/probes covering 3′ and 5′ end; NA: Not Analyzable; ND: Not Determined; +: fusion detected; −: fusion not detected; ±: fusion uncertain; V1: EML4_13:ALK_20; V2: EML4_20:ALK_20; V3a: EML4_6a:ALK_20; V3b: EML4_6b:ALK_20; V6: EML4_13:ALK_20_ins69