Extended Data Fig. 2: CONSORT diagram for the various biomarker analyses.

^aTwo patients were determined to have hemangioma and solitary fibrous tumor at resection despite initial pathology consistent with NSCLC. ^bIncludes 1 EGFR-positive patient. ^cThe reasons were as follows: clinical progression (n = 3), physician did not want to delay patient surgery (n = 1), physician did not consider the patient a good surgical candidate (n = 1), and physician discontinued patient from the study because of an adverse event (n = 1). ^dOne patient was determined to have preexisting congestive heart failure, 1 declined surgery, and 1 was lost to follow-up. ^eEighty patients provided a total of 98 samples for the bulk RNA-seq analyses (54 at baseline and 44 at surgery). ALK, anaplastic lymphoma kinase; EGFR, epidermal growth factor receptor; ES, exome sequencing; MPR, major pathologic response; NSCLC, non-small cell lung cancer; PD, progressive disease; RECIST, Response Evaluation Criteria in Solid Tumors; RNA-seq, ribonucleic acid sequencing; scRNA-seq, single-cell ribonucleic acid sequencing; TMB, tumor mutational burden.