PMC10248858_01
Total WBC count vs. time. The vertically shaded regions show the dose and schedule of avapritinib over time.
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His-avapritinib was held and restarted at a decreased dose of 100 mg daily, but he again developed neutropenia and thrombocytopenia leading to a brief dose holds and subsequent step wise dose reduction to 100 mg every other day (at that time, 100 mg tablets the smallest available formulation) (Fig. 1).  During therapy, the leukemic cell mutational burden and clone diversity was monitored with next generation sequencing.
Panel A-C. The patients NGS data was clustered using Pairtree, a clone tree reconstruction algorithm. Variants were clustered using the pairwise clustering model. Clusters were visualized using the R package "Timescape".Time 0 = date of first NGS data.  This analysis identified 8 distinct clusters that emerged over time. The original myeloproliferative clone had mutations of MSH6 (likely a benign germline polymorphism), ASXL1 and EZH2 (Clone 1). Subsequently, this clone developed presumed bi-allelic inactivating mutations of TET2 (Clone2). Clone 2 underwent branched evolution with acquisition of a NRAS Y64D mutation in clone 3 and a KIT D816V mutation in clone 4. Avapritinib treatment eradicated clone 4, with the NRAS Y64D clone undergoing additional branched evolution with acquisition of SETBP1 (clone 5), ETV6 (clone 6), or STAG2 mutations (clone 7). Ultimately, the STAG2 clone became extinguished and the NRAS mutant/ETV6 clone acquired additional NRAS and SMC1A mutations.. Panel D. Variant allele frequency over time with avapritinib treatment. Specific mutations identified: MSH6 p.E1121K, ASXL1 p.G646fs*12, EZH2 p.S669G, TET2 -1 p.R1452*, TET2-2 p.V1864fs*23, NRAS-1 p.Y64D, KIT p.D816V, SETBP1 p.G870S, ETV6 p.P214L, STAG2 p.R1045*, NRAS-2 p.G12V, SMC1A  p.R807H. TET2-1 and TET2-2 VAFs were added together to model presumed bi-allelic inactivation of TET-2 and the combined VAF value was plotted.
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Patient remained stable on this dose for 8 more months with normalization of his white count and continued decrease in KIT D816 allele frequency from 22% to 13% and finally 2% (Figs. 2).  After almost 17 total months of avapritinib therapy, he redeveloped leukocytosis, thrombocytopenia, and anemia and his avapritinib dose was increased to 100 mg daily.