Impact of the variant allele frequency of ASXL1, DNMT3A, JAK2, TET2, TP53, and NPM1 on the outcomes of patients with newly diagnosed acute myeloid leukemia

Cancer. 2020 Feb 15;126(4):765-774. doi: 10.1002/cncr.32566. Epub 2019 Nov 19.

Abstract

Background: The impact of the allelic burden of ASXL1, DNMT3A, JAK2, TET2, and TP53 mutations on survival remains unclear in patients with newly diagnosed acute myeloid leukemia (AML).

Methods: The authors assessed bone marrow aspirates from 421 patients with newly diagnosed AML using next-generation sequencing for ASXL1, DNMT3A, JAK2, TET2, and TP53 mutations, defined as the presence of mutations in ASXL1, DNMT3A, JAK2, TET2, or TP53 with a minimum variant allele frequency (VAF) of 5%.

Results: A total of 71 patients (17%) had ASXL1 mutations, 104 patients (25%) had DNMT3A mutations, 16 patients (4%) had JAK2 mutations, 82 patients (20%) had TET2 mutations, and 86 patients (20%) had TP53 mutations. Among patients with each mutation, the median VAF of ASXL1 was 34.31% (range, 1.17%-58.62%), the median VAF of DNMT3A was 41.76% (range, 1.02%-91.66%), the median VAF of JAK2 was 46.70% (range, 10.4%-71.7%), the median VAF of TET2 was 42.78% (range, 2.26%-95.32%), and the median VAF of TP53 was 45.47% (range, 1.15%-93.74%). The composite complete response rate was 60%, and was 77% in patients with AML with and without ASXL1, DNMT3A, JAK2, TET2, or TP53 mutations, respectively (P = .006); the median overall survival was 11 months and 27 months, respectively (P < .001). Multivariate analysis identified age; an antecedent history of dysplasia; white blood cell count; adverse cytogenetic risk; previous treatment with an FLT3 inhibitor; and the VAF of ASXL1, DNMT3A, JAK2, TET2, TP53, and NPM1 mutations by next-generation sequencing as prognostic factors for overall survival.

Conclusions: The VAF of ASXL1, DNMT3A, JAK2, TET2, TP53, and NPM1 mutations is associated with worse prognosis in patients with newly diagnosed AML.

Keywords: ASXL1; DNMT3A; JAK2; TET2; TP53; acute myeloid leukemia.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acute Disease
  • Biomarkers, Tumor / genetics*
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA Methyltransferase 3A
  • DNA-Binding Proteins / genetics
  • Dioxygenases
  • Female
  • Gene Frequency
  • Genetic Predisposition to Disease / genetics*
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Janus Kinase 2 / genetics
  • Kaplan-Meier Estimate
  • Leukemia, Myeloid / diagnosis
  • Leukemia, Myeloid / genetics*
  • Male
  • Middle Aged
  • Mutation*
  • Nuclear Proteins / genetics
  • Nucleophosmin
  • Prognosis
  • Proto-Oncogene Proteins / genetics
  • Repressor Proteins / genetics
  • Retrospective Studies
  • Tumor Suppressor Protein p53 / genetics

Substances

  • ASXL1 protein, human
  • Biomarkers, Tumor
  • DNA-Binding Proteins
  • DNMT3A protein, human
  • NPM1 protein, human
  • Nuclear Proteins
  • Proto-Oncogene Proteins
  • Repressor Proteins
  • Tumor Suppressor Protein p53
  • Nucleophosmin
  • Dioxygenases
  • TET2 protein, human
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA Methyltransferase 3A
  • JAK2 protein, human
  • Janus Kinase 2