TP53 mutations with low variant allele frequency predict short survival in Chronic Lymphocytic Leukemia

Purpose. In chronic lymphocytic leukemia (CLL), TP53 mutations are associated with reduced survival and resistance to standard chemo-immunotherapy (CIT). Nevertheless, the clinical impact of subclonal TP53 mutations below 10-15% variant allele frequency (VAF) remains unclear. Experimental Design. Using a training/validation approach, we retrospectively analyzed the clinical and biological features of TP53 mutations above (high-VAF) or below (low-VAF) the previously reported 10.0% VAF threshold, as determined by deep next-generation-sequencing (NGS). Clinical impact of low-VAF TP53 mutations was also confirmed in a cohort (n=251) of CLL treated with FCR or FCR-like regimens from two UK trials. Results. In the training cohort 97/684 patients bore 152 TP53 mutations while in the validation cohort 71/536 patients had 109 TP53 mutations. In both cohorts, TP53 mutated patients experienced significantly shorter overall survival (OS) than TP53 wild-type (wt) patients, irrespective of the TP53 mutation VAF. By combining TP53 mutation and 17p13.1 deletion (del17p) data in the total cohort (n=1,220), 113 cases were TP53 mutated only (73/113 with low-VAF mutations), 55 del17p/TP53 mutated (3/55 with low-VAF mutations), 20 del17p only, and 1,032 (84.6%) TP53wt. A model including low-VAF cases outperformed the canonical model, which considered only high-VAF cases (c-indices 0.643 vs. 0.603, P<0.0001), and improved the prognostic risk stratification of CLL-IPI. Clinical results were confirmed in CIT-treated cases (n=552) from the retrospective cohort, and the UK trials cohort. Conclusion. TP53 mutations impacted OS irrespective of VAF. This finding can be used to update the definition of TP53 mutated CLL for clinical purposes.