Supplementary Figure 6: MICA amplification in TCGA samples and the associations with gene expression, IgG1/3 level, and patient survival.

a, MICA amplification in paired normal and tumor samples. The table summarizes the number of patients with different MICA amplification status in paired tumor and adjacent normal tissues. MICA AMP means amplification in the MICA/MICB genes, and MICA WT means no amplification. b, MICA amplification correlated with gene expression differences (n = 9,846). Box plots show the differential expression of MICA, ADAM17, and MMP14 in tumors with or without MICA amplifications, where the boxes show the lower, median, and upper quartiles of values, and lines extend to 1.5 times the interquartile range. Statistical significance was evaluated using Wilcoxon rank sum test. c, IgG1/3 level in tumor samples with or without MICA amplification (n = 5,104). The boxplot shows the distribution of the IgG1/3 switch level in tumor samples with or without MICA amplification. Statistical significance was evaluated using Wilcoxon rank sum test (two-sided P value). Box plots show the lower, median, and upper quartiles of values, and lines extend to 1.5 times the interquartile range. d, Kaplan–Meier curve shows the survival differences in all TCGA patients with or without MICA amplification (n = 7,147). e, For each tumor type, hazard ratios and statistical significance from Wald test were evaluated using Cox proportional hazard regressions corrected for tumor purity and patient age. f, High- or low-IgG1/3 groups were split by the median value of IgG1/3 levels in each MICA group (see Supplementary Table 3 for sample sizes). The IgG1/3 level was the number of IgG1 or IgG3 B cell clusters normalized by the total number of unique CDR3s. Hazard ratios and statistical significance were evaluated using Cox proportional hazard regressions corrected for tumor purity and patient age. FDR correction was performed using the Benjamini–Hochberg procedure for testing on multiple cancer types.