Genomic Analysis of Therapeutic Response

Correlations between mutations and response to therapy were assessed by the Fisher exact test and trend test across the response groups (prop.trend.test function in R). Comparison of continuous variables between groups was performed by the Mann-Whitney rank test, while the Wilcoxon rank test was used for paired samples. Survival data were assessed by a Cox regression analysis, calculating hazard ratios for each parameter. For Kaplan-Meier plots, patient subgroups were compared by the log rank test (for further details, see Additional file 1). Genomic Identifications of Significant Targets in Cancer (GISTIC) 2.0 [35 (link)] was used to identify frequent focal- and arm-level amplifications and deletions.
Statistical analyses were performed using R, version 3.6.3, or the SPSS 26/PASW 17.0 software package. All p-values reported are two-tailed, and p < 0.05 was considered statistically significant.