Prognostic significance of serial molecular annotation in myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (sAML)

Abstract

The implementation of next-generation sequencing (NGS) has influenced diagnostic, prognostic, and therapeutic decisions in myeloid malignancies. However, the clinical relevance of serial molecular annotation in patients with myelodysplastic syndrome (MDS) undergoing active treatment is unknown. MDS or secondary acute myeloid leukemia (sAML) patients who had at least two NGS assessments were identified. Outcomes according to mutation clearance (NGS-) on serial assessment were investigated. Univariate and multivariate Cox regression models were used to evaluate the prognostic impact of NGS trajectory on overall survival (OS). A total of 157 patients (MDS [n = 95]; sAML [n = 52]; CMML [n = 10]) were identified, with 93% of patients receiving treatment between NGS assessments. Magnitude of VAF delta from baseline was significantly associated with quality of response to treatment. Patients achieving NGS- had significantly improved OS compared to patients with mutation persistence (median OS not reached vs. 18.5 months; P = 0.002), which was confirmed in multivariate analysis (HR,0.14; 95%CI = 0.03-0.56; P = 0.0064). Serial TP53 VAF evaluation predicts outcomes with TP53 clearance representing an independent covariate for superior OS (HR,0.22; 95%CI = 0.05-0.99; P = 0.048). Collectively, our study highlights the clinical value of serial NGS during treatment and warrants prospective validation of NGS negativity as a biomarker for treatment outcome.

Fig 1.. Dynamics of VAF changes of dominant clone before and after treatment.

(A) VAF of the dominant clone is shown for patients before and after therapy with HMA, chemotherapy or BMT. (B, C, E) VAF change of the dominant clone based on disease status at time of serial analysis. HI⁺ includes HI, partial remission and marrow CR per IWG 2006 criteria. (D, F) Comparison of VAF change in patients who achieve CR versus other response (HI⁺/CRi) versus no response. Mann-Whitney (B, C, E) and Kruskal-Wallis (D, F) tests were utilized for the comparative analyses of VAF changes. Abbreviations: VAF, variant allele frequency; NGS, next generation sequencing; HMA, hypomethylating agent, BMT, allogeneic stem cell transplant; CR complete remission; CRi, CR with incomplete hematologic recovery; HI, hematologic improvement.

Fig 2.. Mutational spectrum in patients who achieved NGS negativity on serial analyses.

A total of 21 patients achieved NGS negativity during the study period. Patient number is listed on the first column with each colored box representing a mutation of the gene listed in that column. Mutations are grouped by class of mutation. Insert arrow on the right represents treatment between NGS assessments. Abbreviations: HMA, hypomethylating agents; CTx, chemotherapy; BMT, allogeneic stem cell transplant; DLI, donor lymphocyte infusion.

Fig 3.. Prognostic impact of serial NGS results on overall survival.

(A) OS of patients stratified by NGS positive versus NGS negative disease at any point and (B) at the last assessment. OS of patients stratified by gain of mutation (C), VAF increase (D), or loss of a mutation (E). (F) OS of patients who lost a mutation with exclusion of patients who became NGS negative. Abbreviations: OS, overall survival; NGS, next generation sequencing; VAF, variant allele frequency.

Fig 4.. Prognostic impact of TP53 VAF changes on overall survival.

(A) OS of TP53 mutant patients who have a durable VAF <20% on serial assessment versus patients with a VAF ≥20% at baseline or who had VAF expansion to ≥20% on serial assessment. (B) Further stratification based on TP53 mutant patients who became TP53 mutation negative (<5% VAF). Abbreviations: VAF, variant allele frequency; NGS, next generation sequencing.