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Background    EML4-ALK  fusion gene is found in only a small subset (2–6%) of non-small cell lung cancer. There is an urgent need to establish a rational diagnostic algorithm to identify this rare but important fusion in lung cancer.    Methods  We performed a comprehensive analysis of  EGFR/KRAS  mutation and  ALK  rearrangement in a total of 360 surgically resected lung cancers.  ALK  rearrangement was examined by 3 analyses: multiplex reverse transcription-PCR, fluorescent  in situ  hybridization (FISH), and immunohistochemistry (IHC) with the intercalated antibody-enhanced polymer method. A scoring system was used for IHC (iScore). A test set (202 patients with unselected lung cancer) was used for proposing a diagnostic algorithm. This diagnostic algorithm was validated in 158 patients with  EGFR  and  KRAS  mutation-negative adenocarcinoma.    Results    ALK  rearrangement was identified in 2 patients (1.0%) from the test set and both adenocarcinomas were negative for  EGFR  and  KRAS  mutations. The results of FISH and RT-PCR were completely matched. The highest iScore 3 was found only in the 2 positive cases. A diagnostic algorithm was proposed: IHC screening for  ALK  rearrangement followed by confirmatory FISH. In the validation set, 8 cases (5.1%) had iScore 3 and were positive for FISH, while the other cases had iScore 0 and were negative for FISH.    Conclusions  Screening for  ALK  rearrangement by IHC followed by confirmatory FISH is a rational diagnostic algorithm. If needed, patients may be selected for screening  ALK  rearrangement by their  EGFR  and  KRAS  mutation status.

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A Rational Diagnostic Algorithm for the Identification of ALK Rearrangement in Lung Cancer: A Comprehensive Study of Surgically Treated Japanese Patients