We systematically applied this approach to five other major solid tumor types, and demonstrate that multiple impactful clinical features vary by the site for all tumor subtypes tested—including ALK fusion status in squamous cell lung cancer (LUSC TCGA cohort, n = 155) and lung adenocarcinoma (LUAD TCGA cohort, n = 112) and human papillomavirus (HPV) status in head and neck squamous cell carcinoma (HNSC TCGA cohort, n = 332)—all with P < 0.05 and significant after FDR correction (Supplementary Table 1 and Supplementary Fig. 1). Here, ALK is linked to head and neck squamous cell carcinoma.