Treatment-emergent mutations at 24 months. (A) Number of treatment-emergent mutations at 24 months. Thirty-eight treatment-emergent mutations were detected in 32 patients, 4 of whom had discontinued treatment. Mutations were defined as treatment-emergent if: (1) the VAF was <0.01 in the baseline sample and ≥0.01 in the 24-month sample (n = 36); or (2) if the VAF was ≥0.01 in the baseline sample and had a more than fourfold increase in the 24-month sample (n = 2). The most frequent treatment-emergent mutations were detected in DNMT3A (n = 15 [39%]), followed by TET2 (n = 4 [11%]), ASXL1 (n = 3 [8%]), PPM1D (n = 3 [8%]), and TP53 (n = 3 [8%]). (B) VAF of treatment-emergent mutations at baseline and posttreatment at 24 months. The median VAF of treatment-emergent mutations was low (median, 1.5%) and primarily occurred in JAK2-mutated patients (97%). Representative examples of treatment-emergent mutations detected in patients treated with HU (C) and IFNα (D). MPN phenotypic driver mutations are depicted with blue lines, treatment-emergent concomitant mutations with red lines, and other concomitant mutations with black lines. The upper rows of panels C and D also show uniparental disomy of chromosome 9p (9p-UPD) analysis. In all examples, 9p-UPD is no longer detectable posttreatment at 24 months, which is concordant with the decrease in mutant JAK2 VAF.