4.14. Statistical Analysis

Areas of the genome with a statistically high frequency of aberration (p-value ≤ 0.05) were identified using the Genomic Identification of Significant Targets in Cancer (GISTIC) tool [27] in Nexus Copy Number software. The CNA frequency reported as being significantly different between the two groups met a minimum p-value of 0.05 on a two-tailed Fisher’s exact test. Patients who did not experience a PFS event (i.e., disease progression, clinical progression, or death) were censored. As this was a single-arm study, no comparative efficacy analyses were performed. The log-rank statistic was used to identify regions yielding a high degree of progression-free survival prediction [70]. The p-value is calculated by permuting the PFS time for each sample and comparing the log-rank statistic for the permuted data to the original data. The threshold used was a p-value ≤ 0.05. Kaplan–Meier curves were generated to compare survival times between two groups, and p-values were computed using the log-rank test. Cox regression was used to evaluate possible confounding variables for baseline characteristics and duration of response correlation analysis.