Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia

Abstract

Importance: Tests that predict outcomes for patients with acute myeloid leukemia (AML) are imprecise, especially for those with intermediate risk AML.

Objectives: To determine whether genomic approaches can provide novel prognostic information for adult patients with de novo AML.

Design, setting, and participants: Whole-genome or exome sequencing was performed on samples obtained at disease presentation from 71 patients with AML (mean age, 50.8 years) treated with standard induction chemotherapy at a single site starting in March 2002, with follow-up through January 2015. In addition, deep digital sequencing was performed on paired diagnosis and remission samples from 50 patients (including 32 with intermediate-risk AML), approximately 30 days after successful induction therapy. Twenty-five of the 50 were from the cohort of 71 patients, and 25 were new, additional cases.

Exposures: Whole-genome or exome sequencing and targeted deep sequencing. Risk of identification based on genetic data.

Main outcomes and measures: Mutation patterns (including clearance of leukemia-associated variants after chemotherapy) and their association with event-free survival and overall survival.

Results: Analysis of comprehensive genomic data from the 71 patients did not improve outcome assessment over current standard-of-care metrics. In an analysis of 50 patients with both presentation and documented remission samples, 24 (48%) had persistent leukemia-associated mutations in at least 5% of bone marrow cells at remission. The 24 with persistent mutations had significantly reduced event-free and overall survival vs the 26 who cleared all mutations. Patients with intermediate cytogenetic risk profiles had similar findings. [table: see text].

Conclusions and relevance: The detection of persistent leukemia-associated mutations in at least 5% of bone marrow cells in day 30 remission samples was associated with a significantly increased risk of relapse, and reduced overall survival. These data suggest that this genomic approach may improve risk stratification for patients with AML.

Figure 1

Flowchart Outlining the Selection of Samples and Sequencing Approaches in the Study ^aAML-RMG is a capture reagent consisting of all of the exons of the genes that are currently known to be recurrently mutated in acute myeloid leukemia, based on The Cancer Genome Atlas AML study. ^bThe only samples with sufficient day 30 DNA for sequencing and assessment of disease clearance (refractory group, 6 patients; R6-12 group, 8 patients; LFR group, 11 patients). ^c Enhanced exome sequencing is exome capture-based sequencing supplemented with the AML-RMG panel of target genes, to improve coverage of critical regions of the exome. ^d Targeted Ampliseq is a polymerase chain reaction–based digital sequencing approach that allows for accurate determination of the frequency of specific mutations in acute myeloid leukemia samples.

Figure 2

Clearance Patterns of Acute Myeloid Leukemia–Associated Mutations Detected by Exome Sequencing VAF indicates variant allele frequency. Panels A through D show examples of different patterns of clearance of leukemia-associated mutations after induction therapy in 4 acute myeloid leukemia cases. Key leukemic variants are highlighted by labels and color. All patients had a morphologic complete remission in the approximately day 30 sample (thick gray line shows that blast counts declined to <5%on approximately day 30 for all cases). The patterns include complete clearance of all variants at day 39 that remain undetectable during an extended remission (>1 year) (panel A); incomplete clearance of most variants at day 31, with subsequent return of these mutations at relapse on day 90 (panel B); clearance of subclonal variants at day 32 (panel C) or day 39 (panel D), with persistence of founding clone variants that remain present at relapse (eg, TET2 for panel C and DNMT3A and IDH2 for panel D). Panels E and F, for the 25 samples with follow-up exome sequencing, the clearance patterns of all leukemia-associated variants detected on day 0 are separately shown for patients with an event-free survival of 12 months or less (n = 16, panel E) or more than 12 months (n = 9, panel F). ^a The high TET2 VAF levels (75%–90%) in panel C suggest that 1 copy of TET2 was probably deleted in the founding clone of this acute myeloid leukemia sample.

Figure 3

Day 30 Mutation Clearance Patterns by Patient for 50 Acute Myeloid Leukemia Cases AML indicates acute myeloid leukemia; AML-RMG, recurrently mutated AML genes; EFS, event-free survival; VAF, variant allele frequency. Top: bar plots showing the number of mutations assessed at day 30, color coded according to whether they exceeded the day 30 VAF threshold of 2.5%. Mutations that occurred in AML-RMG are labeled with white diamonds. The panel is divided into samples with at least 1 variant with a day 30 VAF of 2.5%or more (left) and samples in which the day 30 VAF for all mutations was less than 2.5% (right). Bottom: key AML genes and pathways, showing patterns of mutations and clearance. ^a Three cases that received an allogeneic transplant in the first complete remission. Exclusion of these 3 cases from the analysis did not significantly alter the outcome results. ^b The median event-free survival of cases with a day 30 VAF of less than 2.5% for all mutations was 17.9 months vs 6.0 months for the cases in which at least 1 variant persisted with a VAF threshold of 2.5%or more (P < .001).

Figure 4

Day 30 Mutation Clearance by Gene for 50 Acute Myeloid Leukemia Cases VAF indicates variant allele frequency. Serial VAF measurements demonstrating the clearance patterns of several recurrently mutated acute myeloid leukemia genes in the set of 50 cases. Orange lines indicate a day 30 VAF of 2.5%or more; blue lines indicate a day 30 VAF of less than 2.5%.

Figure 5

Association Between Mutation Clearance and Outcomes AML indicates acute myeloid leukemia; VAF, variant allele frequency. Data were censored at last contact or at January 21, 2015.