Mutations with Low Variant Allele Frequency Predict Short Survival in Chronic Lymphocytic Leukemia.

Purpose: In chronic lymphocytic leukemia (CLL), mutations are associated with reduced survival and resistance to standard chemoimmunotherapy (CIT). Nevertheless, the clinical impact of subclonal mutations below 10% to 15% variant allele frequency (VAF) remains unclear.

Experimental Design: Using a training/validation approach, we retrospectively analyzed the clinical and biological features of mutations above (high-VAF) or below (low-VAF) the previously reported 10.0% VAF threshold, as determined by deep next-generation sequencing. Clinical impact of low-VAF mutations was also confirmed in a cohort ( = 251) of CLL treated with fludarabine-cyclophosphamide-rituximab (FCR) or FCR-like regimens from two UK trials.

Results: In the training cohort, 97 of 684 patients bore 152 mutations, while in the validation cohort, 71 of 536 patients had 109 mutations. In both cohorts, patients with the mutation experienced significantly shorter overall survival (OS) than wild-type patients, regardless of the mutation VAF. By combining mutation and 17p13.1 deletion (del17p) data in the total cohort ( = 1,220), 113 cases were mutated only (73/113 with low-VAF mutations), 55 del17p/ mutated (3/55 with low-VAF mutations), 20 del17p only, and 1,032 (84.6%) wild-type. A model including low-VAF cases outperformed the canonical model, which considered only high-VAF cases (c-indices 0.643 vs. 0.603, < 0.0001), and improved the prognostic risk stratification of CLL International Prognostic Index. Clinical results were confirmed in CIT-treated cases ( = 552) from the retrospective cohort, and the UK trials cohort.

Conclusions: mutations affected OS regardless of VAF. This finding can be used to update the definition of mutated CLL for clinical purposes.