Unique copy number alterations identified from lpWGS are associated with post-CART19 outcomes. (A) GISTIC analysis of copy number alteration profiles of 122 patients identified 11 peaks of DNA copy gain (red) and 23 peaks of DNA copy loss (blue). The green line denotes the significance threshold of q-value = 0.25. The number of patients harboring each lesion from the set of 108 patients included in the outcome analysis is shown. Hazard ratios with 95% confidence intervals from univariate Cox regression analysis of the association are shown for each CNA and PFS for the 108 patients with detected copy number alterations. False discovery rate (FDR) values after Bonferroni correction of Cox regression analysis. The dashed line denotes the significant threshold of FDR = 0.1. The 3 copy number alterations significantly associated with PFS (in order of increasing FDR value) were deletion 10q23.31, deletion 11q25, and deletion 14q32.2. (B-C) Kaplan Meier plots of PFS (B) and OS (C) stratified by presence or absence of deletion 10q23.31 as detected by GISTIC demonstrate that the patients with deletion 10q23.31 (n = 12, 11%) experienced significantly worse PFS and OS compared with those without 10q23.31 deletions (n = 96, 89%).