Immune and Tumor Profiling in NSCLC and Follicular Lymphoma

All patient samples in this study were collected with informed consent for research use and were approved by the Stanford Institutional Review Board in accordance with the Declaration of Helsinki. For a patient with metastatic NSCLC treated with an immune checkpoint inhibitor (Pembrolizumab, Merck), peripheral blood was obtained on the first day of treatment prior to infusion (Fig. 2a; NCT00349830 and NCT02955758). Fresh tumor biopsies from patients with early stage NSCLC were obtained during routine primary surgical resection (Figs. 3g and 5, Supplementary Fig. 13c-f). Fresh or frozen surgical biopsies of follicular lymphoma tumors were obtained from previously untreated FL patients enrolled in a phase III clinical trial (NCT00017290^{63 (link)}), as well as from patients seen as part of the Stanford University Lymphoma Program Project (NCT00398177; Figs. 3b-f, 5a-c, Supplementary Figs. 6a-c, 14). Whole blood samples from 12 healthy adult donors were obtained from the Stanford Blood Center (Fig. 2b,e and Supplementary Figs. 1d,k,l, 2a,d).