Inference of immune cell infiltration and signature score

We integrated several computational tools ^31-35 (Supplementary Methods) to estimate immune infiltration in the IMvigor210 and TCGA RNA-seq cohorts. Using the gsva algorithm, GO ³⁶, KEGG ³⁷, REACTOME ³⁸, and HALLMARK ³⁹ gene sets were employed to estimate pathway enrichment scores for each sample. Other prevalent gene signature scores with respect to tumor microenvironment, tumor intrinsic pathway, and metabolism were calculated for each sample using the PCA algorithm ^{9, 39} (see the detailed procedure in the Supplementary Methods).