Figure 2.

Immune cell infiltration in patient samples from clinical study CheckMate 038. A) Box plot the MCP-Counter T cell score according to response to therapy combining all treatment groups using an optimal pooled t-test since data is paired and unpaired. B) Principal component analysis showing all RNAseq samples, paired and unpaired, plotted on the first two components. The size of the data point is proportional to the T cell score. Open circles correspond to pre-treatment samples, while closed circles correspond to on-treatment samples. The data points are colored by response (Red = PD, Green = SD, and Blue = CRPR). The vector for the T cell score is plotted as well. Outlier samples are labeled by case. The twelve paired outlier samples were either due to quality control issues that had not been detected, or may be due to an actual different biology. For example, cases 48, 20038, and 30022 all had interferon-gamma signaling either going down or not changing on treatment, while cases 30004 and 20001 have G2M cell cycle genes that either increase or did not respond. C) Box plots showing the average expression of the genes correlated with the T cells broken down by response and pre- and on-treatment using an optimal pooled t-test since data is paired and unpaired. D) Box plots of MCP-Counter immune cell deconvolution types according to response to therapy. Mixed t-test for paired and unpaired samples using an optimal pooled t-test since data is paired and unpaired (*p value < 0.05, **p value < 0.01, ***p value < 0.001, ****p value < 0.0001). See also Figures S3, S4 and S5.