FLT3,   NPM1

Pooled analysis of associations between karyotype and outcome in NPM1-mutated AML

According to the 2017 European LeukemiaNet (ELN) guidelines, mutations in the nucleophosmin 1 (NPM1) gene are associated with a favorable prognosis in acute myeloid leukemia (AML) when an internal tandem duplication (ITD) in the fms-related tyrosine kinase 3 gene (FLT3) is not present (FLT3-ITDneg), or is present with a low (<0.5) allelic ratio (FLT3-ITDlow).1

The ELN 2017 guidelines also consider the NPM1mut/FLT3-ITDneg/low status favorable regardless of co-existing chromosomal abnormalities. To investigate this further, Linus Angenendt, University Hospital Münster, Münster, DE and colleagues, evaluated the potential prognostic impact of karyotypes in intensively-treated patients with NPM1mut/FLT3-ITDneg/low AML in a pooled analysis of data from study groups or treatment centers worldwide.2

Study design
  • Individual patient data were collected from nine international AML study group registries or treatment centers
  • Intensively-treated patients with a known karyotype and who carried an NPM1 mutation in the absence of an FLT3-ITD mutation with a high (≥5) allelic ratio were included
  • Data on intensively-treated patients with NPM1 wild type (NPM1wt) and adverse cytogenetics (as defined in ELN 2017 guidelines1) were used as an adverse-risk reference cohort
  • A minimal data set was collected for each patient including age, sex, date of AML diagnosis, type of AML (de novo or secondary), bone marrow (BM) blast count, white blood cell (WBC) count, karyotype, NPM1/FLT3-ITD mutational status including mutant/wild-type ratio, type of and response to induction chemotherapy, date of allogeneic HSCT in first complete remission (CR1), date of allogeneic HSCT beyond CR1, events (induction failure, relapse, death), and date of last contact
  • All karyotypes were centrally reviewed by a hematologist and a geneticist following the International System for Human Cytogenomic Nomenclature 2016 guidelines.3
  • As per the ELN 2017 guidelines,1 cytogenetic abnormalities were classified as favorable, intermediate or adverse

Patient characteristics

  • N=2,426 patients with NPM1mut/FLT3-ITDneg/low AML
    • N=2,000 patients (82.4%) with normal karyotype
    • N=426 patients (17.6%) with an abnormal karyotype
      • N=329 patients (13.6%) with chromosomal abnormalities of intermediate-risk
      • N=83 patients (3.4%) with chromosomal abnormalities of adverse risk
      • N=14 patients (0.6%) with favorable core-binding factor cytogenetics
    • N=1,845 patients with NPM1wt/FLT3-ITDneg/low AML and adverse-risk cytogenetics
    • Selected baseline characteristics are in Table 1
    • In patients with NPM1mut/FLT3-ITDneg/low AML, the presence of adverse-risk cytogenetics was associated with older age, male sex, secondary AML, and negative FLT3-ITD status
    • Compared to patients with NPM1wt/FLT3-ITDneg/low with adverse cytogenetics, patients with NPM1mut/FLT3-ITDneg/low with adverse cytogenetics were older, had higher bone marrow (BM) blast counts, and had higher WBC counts
    • Rearrangements of 11q23, -5/del(5q), and a monosomal karyotype were underrepresented in patients with NPM1mut/FLT3-ITDneg/low with adverse-risk karyotype compared with the NPM1wt/FLT3-ITDneg/low reference group
 Table 1. Selected baseline characteristics 
  NPM1-mutated karyotype NPM1-wild type karyotype
Characteristic Normal Intermediate Adverse P* Adverse P
No. patients 2,000 329 83   1845  

Age (years)

Median age (range)

56 (18–84)

56 (18–83)

62 (28–79)
58 (18–85)



875 (43.8)

181 (55)

50 (60.2)
1,007 (54.6)

AML type

De novo



1,805 (90.2)

176 (8.8)1

9 (0.9)

294 (89.4)

35 (10.6)


68 (81.9)

14 (16.9)

1 (1.2)


1,350 (73.2)

456 (24.7)

39 (2.1)

WBC, x109/LMedian, (range)
20 (0–453)

18 (1–339)

14 (0–221)
5 (0–468)

BM blasts

Median, (range)

66 (0–100)

66 (2–99)

67 (16–96)
52 (1–100)



Present with a low allelic ratio


1,592 (79.6)

408 (20.4)


292 (88.8)

37 (11.2)


80 (96.4)

3 (3.6)



1,799 (97.5)

46 (2.5)


Allogeneic HSCT






1,409 (70.5)

330 (16.5)

254 (12.7)

7 (0.4)


225 (68.4)

67 (20.4)

37 (11.2)



58 (69.9)

17 (20.5)

8 (9.6)





441 (23.9)

321 (17.4)

9 (0.5)


Adverse cytogenetic abnormalities
















17 (20.5)

15 (18.1)

21 (25.3)

59 (71.1)



41 (2.2)

182 (9.9)

29 (1.6)

106 (5.7)


509 (27.6)

461 (25)

859 (46.6)

1,129 (61.2)











Note: Data are No. (%) unless otherwise stated

HSCT, hematopoietic stem cell transplantation

*P values for comparison of characteristics in patients with NPM1 mutations according to cytogenetic risk.

†P values for comparison of characteristics in patients with adverse cytogenetics according to NPM1 mutational status.

‡Karyotype with cytogenetic aberrations classified as neither favorable nor adverse risk.

§Kruskal-Wallis or Mann-Whitney test.

x2 test.

Fisher’s exact test.

Karyotype and outcome in NPM1mut/FLT3-ITDneg/low AML
  • Median follow-up time for all patients was 4.23 years (95% CI, 05–4.46)
  • See Table 2. In patients with NPM1mut/FLT3-ITDneg/low AML, adverse cytogenetics were associated with:
    • Lower CR rates compared with a normal or intermediate-risk karyotype (P<0.001)
      • Similar CR rate to patients with NPM1wt/FLT3-ITDneg/low with adverse cytogenetic abnormalities (57.5%; P=0.11)
    • Inferior 5-year overall survival (OS) compared with a normal or intermediate-risk karyotype (P<0.001)
    • Inferior event-free survival (P<0.001)
    • A higher 5-year cumulative incidence of relapse (CIR; P=0.0012)
Table 2. Karyotype and outcome in NPM1mut/FLT3-ITDneg/low AML
  NPM1-mutated karyotype
Outcomes Normal(n=2000) Intermediate(n=329) Adverse(n=83)
CR rate 87.7% 86% 66.3%
5-year OS rate 52.4% 44.8% 19.5%
Median OS, years 6.62 2.99 0.63
5-year EFS 40.6% 36% 18.1%
Median EFS, years 2.13 1.45 0.43
CIR 43.6% 44.2% 51.9%
  • When adjusting for age, AML type, WBC, and FLT3-ITD status in multivariable regression analyses:
    • Compared with patients of a normal karyotype, patients with NPM1mut/FLT3-ITDneg/low with adverse cytogenetics had:
      • Reduced likelihood of achieving a CR (odds ratio [OR], 0.29; 95% CI, 0.17–0.48; P<0.001)
      • Increased risk of death (hazard ratio [HR], 2.97; 95% CI, 2.29–3.87; P<0.001)
      • Increased risk of experiencing an event (HR, 2.63; 95% CI, 2.05– 3.38; P<0.001)
      • Increased risk of relapse (HR, 2.52; 95% CI, 1.75– 3.62; P<0.001)
    • When comparing patients with NPM1wt/FLT3-ITDneg/low and NPM1mut/FLT3-ITDneg/low with adverse-risk, there was no significant hazard risk of death (P = 0.77), experiencing an event (P=0.68), or relapse (P=0.53)
    • Comparing intermediate and normal cytogenetics in patients with NPM1mut/FLT3-ITDneg/low, intermediate cytogenetics were associated with inferior OS (HR, 1.27; 95% CI, 1.07 to 1.5; P=0.006) and EFS (HR, 1.21; 95% CI, 1.04 to 1.41; P=0.014), but not with a higher CIR (HR, 1.18; 95% CI, 0.97 to 1.44; P=0.1)
    • Analysis of data excluding the 448 patients with an FLT3-ITDlow mutation showed that adverse cytogenetic abnormalities were associated with an unfavorable outcome in patients with NPM1mut/FLT3-ITDneg disease (HR for death, 2.94; 95% CI, 2.25– 3.84; HR for event, 2.62; 95% CI, 2.03– 3.38; HR for relapse, 2.45; 95% CI, 1.68–to 3.57; all P<0.001)
      • Notably, the FLT3-ITDlow genotype was virtually absent in the adverse karyotype group regardless of NPM1 mutational status (Table 1)
Cytogenetics and prognosis by subgroup
  • A significant interaction of age with OS according to karyotype abnormalities in patients with NPM1mut/FLT3-ITDneg/low AML (Pinteraction=0.0096)
    • Risk of death associated with adverse cytogenetics: 3.97 in younger patients (<60 years) and 1.95 in older patients (≥60 years)
  • In multivariable analyses:
    • Younger patients with adverse cytogenetics had a reduced likelihood of achieving a CR (OR, 0.29; 95% CI, 0.12–0.71; P=0.0062) and an increased risk of death (HR, 4.71; 95% CI, 3.11–7.14; P<0.001), experiencing an event (HR, 3.56; 95% CI, 2.38– 5.31; P<0.001) or relapse (HR, 4.62; 95% CI, 2.81–7.6; P<0.001) compared with patients with normal cytogenetics
    • In older patients, adverse cytogenetics were associated with inferior CR (OR, 0.28; 95% CI, 0.15–0.52; P<0.001), OS (HR, 2.16; 95% CI, 1.53–3.05; P<0.001), and EFS (HR, 2.07; 95% CI, 1.5– 2.87; P<0.001), but not CIR (HR, 1.43; 95% CI, 0.83–2.46; P=0.2)
  • No significant heterogeneity of associations between cytogenetic risk and OS by sex, type of AML, FLT3-ITD status, WBC, BM blast counts, treatment period, or cohort
  • No differences in the association of individual adverse abnormalities with risk of death when comparing NPM1wt/FLT3-ITDneg/low with NPM1mut/FLT3-ITDneg/low in the five largest adverse-risk cytogenetic subgroups (-5/del(5q); -7; abn(17p); complex karyotype; monosomal karyotype)
 Association of post-remission allogeneic HSCT with survival in NPM1mut/FLT3-ITDneg/low AML
  • Only younger patients (<60 years) were included in the analyses due to low frequency of allogeneic HSCT in older patients in CR1
  • N=1,345/1,466 younger patients achieved a CR
    • N=345 (25.7%) patients received an allogeneic HSCT
  • Significant baseline characteristics: patients undergoing transplantation in CR1 more frequently had secondary AML or an FLT3-ITD mutation compared with patients who did not undergo transplantation
  • Patients who underwent transplantation had a lower CIR (22.6% vs4%; P<0.001) but a higher non-relapse mortality (NRM; 18.3% vs 7.4%; P<0.001) compared with patients who did not undergo transplantation in CR1
  • No differences in OS between patients who underwent transplantation and those who did not (65.6% vs2%; P=0.34)
  • In patients with NPM1mut/FLT3-ITDneg/low with adverse cytogenetics:
    • Patients who received allogeneic HSCT in CR1 had a four-fold lower risk of death than patients who did not receive allogeneic HSCT in CR1 (HR, 0.27; 95% CI, 0.09– 0.82; Pinteraction=0.012)
    • There was no significant impact of cytogenetics and post-remission treatment (transplantation vs no transplantation) with CIR or NRM
  • In patients with adverse cytogenetics, the association of allogeneic HSCT in CR1 with better OS was more pronounced in patients with NPM1mut (HR for death, 0.27; 95% CI, 0.09–0.82; Pinteraction=0.012) than in patients with NPM1wt (HR for death, 0.71; 95% CI, 0.58 to 0.87; Pinteraction=0.073)
  • Concomitant chromosomal abnormalities were significantly associated with prognosis in patients with NPM1mut/FLT3-ITDneg/low AML
  • When adverse-risk cytogenetics were present, patients with NPM1mut had a similar unfavorable prognosis as patients with NPM1wt
  • In patients with NPM1mut/FLT3-ITDneg/low AML with adverse cytogenetics, allogeneic HSCT in CR1 was associated with a significantly improved survival compared with consolidation chemotherapy. The authors’ emphasized that these patients should be classified as high-risk and managed as such
  • Due to the retrospective nature of the study, the results should be validated within prospective trials. In addition, the authors’ noted that some patients were not originally classified according to ELN 2017 guidelines and therefore NPM1/FLT3 genetic analyses may have been underperformed in patients with an aberrant karyotype, and patients with an abnormal karyotype might have been under-represented in the study
  1. DÖhner H., et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129:424–47. DOI: 10.1182/blood-2016-08-733196
  2. Angenendt L., et al. Chromosomal Abnormalities and Prognosis in NPM1-Mutated Acute Myeloid Leukemia: A Pooled Analysis of Individual Patient Data From Nine International Cohorts. Journal of Clinical Oncology. 2019; DOI: 10.1200/JCO.19.00416. [Epub ahead of print]
  3. McGowan-Jordan J, Simons A, Schmid M. ISCN 2016: An International System for Human Cytogenomic Nomenclature. Basel, Switzerland, Karger, 2016 [Accessed on September 23rd 2019]
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