Fig. 2: Clinico-genomic “DeePaN” framework discovered NSCLC subgroups with distinct overall survival outcomes of post-IO treatment.

a Five distinct patient subgroups were discovered by DeePaN, visualized by the 2D UMAP projection of the deep patient graph representation in the latent space. Each data point denotes a patient and colors denote distinct subgroup memberships. b The five subgroups discovered by DeePaN showed overall significant post-IO survival difference by the Kaplan–Meier survival plots (same subgroup color encoding as in a). c Using the overall cohort (1937 patients) as the control, comparison of survival of each subgroup with the overall cohort identified distinct IO beneficial and IO non-beneficial subgroups, demonstrated by a volcano plot (see “Methods”). Each bubble represents a patient subgroup, same subgroup color encoding was used as in a and b, and bubble sizes are proportional to corresponding subgroup patient counts. The x axis represents the difference of the estimated median survival times between a subgroup and the overall cohort. The vertical line marked zero median survival difference, with bubbles on the right of the vertical line showing the tendency of beneficial IO outcomes and bubbles on the left showing the tendency of IO non-beneficial outcomes. y axis is the −(FDR) of the corresponding log-rank test between a subgroup vs. the overall cohort with multiple-comparison adjustment by Benjamini–Hochberg procedure, representing the statistical significance of the observed survival difference. The horizontal dashed line marked the statistical significance cutoff of FDR of 0.05. Two IO non-beneficial subgroups (red and orange) and one IO beneficial subgroup (green) were identified with significantly different post-IO overall survival from the overall cohort. We combined the two IO non-beneficial subgroups (red and orange) into one subgroup since they have similar post-IO survival outcomes. d The IO beneficial and the combined IO non-beneficial subgroup showed significant (P-value of 2.2 × 10⁻¹¹) post-IO survival difference with estimated median survival of 20.35 months and 9.42 months, respectively, by the Kaplan–Meier survival plots.