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Background  Echinoderm microtubule-associated protein-like 4 ( EML4 ) is the canonical anaplastic lymphoma kinase ( ALK ) fusion partner in non-small cell lung cancer (NSCLC), and  ALK -positive patients showed promising responses to ALK tyrosine kinase inhibitors (TKIs). However, studies that comprehensively investigate ALK TKI treatment in patients with different  ALK  fusion patterns are still lacking.    Methods  Ninety-eight  ALK -positive patients with advanced NSCLC were retrospectively studied for their response to crizotinib and subsequent treatments. Comprehensive genomic profiling (CGP) was conducted to divide patients into different groups based on their  ALK  fusion patterns. Non-canonical  ALK  fusions were validated using RNA-sequencing.    Results  54.1% of patients had pure canonical  EML4-ALK  fusions, 19.4% carried only non-canonical  ALK  fusions, and 26.5% harbored complex  ALK  fusions with coexisting canonical and non-canonical  ALK  fusions. The objective response rate and median progression-free survival to crizotinib treatment tended to be better in the complex  ALK  fusion group. Notably, patients with complex  ALK  fusions had significantly improved overall survival after crizotinib treatment (p = 0.012), especially when compared with the pure canonical  EML4-ALK  fusion group (p = 0.010). The complex  ALK  fusion group also tended to respond better to next-generation ALK TKIs, which were used as later-line therapies. Most identified non-canonical  ALK  fusions were likely to be expressed in tumors, and some of them formed canonical  EML4-ALK  transcripts during mRNA maturation.    Conclusion  Our results suggest NSCLC patients with complex  ALK  fusions could potentially have better treatment outcomes to ALK TKIs therapy. Also, diagnosis using CGP is of great value to identify novel  ALK  fusions and predict prognosis.

Complex ALK Fusions Are Associated With Better Prognosis in Advanced Non-Small Cell Lung Cancer