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Monitoring of clonal evolution of AML
>50% decrease after one cycle of induction treatment; for statistical evaluation a partial remission sample was considered as a refractory sample.21 Relapse AML was defined as the recurrence of disease after CR, provided that it was detected in ≥5% blasts in the bone marrow or peripheral blood. The classification of clonal or subclon- al mutation was derived from the variant allele frequency (VAF), which provides information about how many cells in a sample carry a particular variant. The VAF is defined as the ratio of sequence reads carrying the mutation to the total number of reads at a specific nucleotide position. In this study, VAF≥10% discrimi- nates a clonal mutation and VAF<10% a subclonal mutation. Accordingly, the predominant clone is the one with a higher VAF. Also, additional molecular abnormalities (AMA) in patients with refractory or relapsed disease were defined as new mutations not present at diagnosis.
Results
Patient cohorts and clinical-biological characteristics
We observed a dynamic mutational profile along the
A
course of AML evaluation, both for samples from patients refractory to induction treatment (patients 1 to 10; Figure 1A and B) and from patients who relapsed after reaching CR (patients 9 to 23; Figure 1A to C). A detailed description of biological and clinical events, and specific treatments of the patients is reported in the Online Supplementary Appendix.
Mutational landscape at diagnosis and treatment failure
Overall, 71 non-recurrent somatic variants were detected with a median coverage of 1,044 (range, 20–6,123) and a median VAF of 36% (range, 1–95%) (Online Supplementary Table S2). Fifty-one variants (71.8%) were single nucleotide variants (SNV) and 20 (28.2%) were small insertions (n=15) or deletions (n=5). Fifty missense variants were identified, in addition to one stop-gain, one in-frame deletion, four frameshift deletions, 14 frameshift insertions and one non- frameshift insertion.
At diagnosis (n=23), 57 variants were detected with a median of twp (range, 0–5) variants/sample. We did not find any mutations in three patients, either at the beginning of
Figure 1A. Legend on page 2329.
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