ALK and squamous cell carcinoma: Three pairs of transcriptome data (1A/1B, 4A/4B, 6A/6B in Table S3) were excluded from the analysis because of mismatches and heterogeneity of baseline characteristics (i.e., ALK mutation in 1A/1B, squamous cell carcinoma in 4A/4B, E746_A750del/E19del mutations in 6A/6B).