Mechanism of Pathway: Considerations of Cytogenetic and Molecular Mutation Status for Patients with Acute Myeloid Leukemia: A Deeper Look at the Role of Diagnostic and Ongoing Testing Across the Care Continuum

Mechanism of Pathway: Considerations of Cytogenetic and Molecular Mutation Status for Patients with Acute Myeloid Leukemia: A Deeper Look at the Role of Diagnostic and Ongoing Testing Across the Care Continuum

Acute myeloid leukemia (AML) is a heterogeneous disease that is characterized by uncontrolled proliferation of undifferentiated myeloid progenitors.1 While these leukemic blasts accumulate in the bone marrow and peripheral blood, impairment of normal hematopoiesis may lead to a reduction in the number of differentiated myeloid cells (granulocytes, neutrophils, monocytes, erythrocytes, megakaryocytes). Associated symptoms and consequences include anemia, bleeding, and an increased risk for infection.2


Although a relatively rare malignancy, AML is the most common form of acute leukemia found in adults; in the United States, approximately 19,520 individuals will be diagnosed with the disease in 2018.3 In 2015, the age-adjusted incidence rate of AML was 4.3 per 100,000 persons. Based on 2011 to 2015 data, the incidence rate of AML was slightly higher in men than in women at 5.2 and 3.6 per 100,000 persons, respectively.4,5 Median age at diagnosis is 68 years.4 AML accounts for the largest number of annual deaths from leukemia in the United States, and there will be approximately 10,670 deaths attributed to the disease in 2018.3 Death rates in the United States have remained stable from 2005 to 2016, at approximately 2.8 per 100,000 persons.4 However, 5-year survival rates for AML have slowly been improving. Although it was estimated that only 19.2% of individuals survived 5 years if diagnosed with AML in 2000, this increased to 28.1% if diagnosed in 2014.5


The biology of AML is inherently complex, and no single model of pathogenesis would likely apply to all cases. However, it has long been surmised that AML may originate from the oncogenic transformation of either a hematopoietic stem cell or a progeny cell that has reacquired the self-renewal properties of a stem cell.6-8 Some populations of leukemic stem cells (LSCs) are mostly quiescent and thus may contribute to chemotherapy resistance and relapse.9,10 In addition to maintaining the malignant clone, LSCs give rise to progeny that undergo further mutations and genetic events, resulting in a population of genetically diverse competing clones.2,11,12

After 30 years with few therapeutic advances, the past decade has witnessed significant developments in our knowledge of the pathogenesis of AML and, subsequently, in the treatment landscape. Although the pathogenesis of AML has not been completely defined, chromosomal rearrangements and molecular changes have been implicated in its development. Comprehensive genomic analyses have shown that multiple molecular pathways drive progression of this clonal hematopoietic disorder.13-15 Abnormal karyotypes with recurrent chromosomal structural variations have been identified in approximately 45% to 55% of patients with AML.16,17 A study of leukemia genes in 1540 patients in 3 clinical trials of intensive AML treatment identified at least 1 driver mutation in 96% of patients and ≥2 driver mutations in 86% of patients.14 Mutations in genes that encode epigenetic modifiers, such as DNMT3A, ASXL1, and TET2, are often acquired early and are present in the founding clone.13,14,18 However, in the general population, these mutations are also found to be acquired as a function of age and do not always result in the development of disease.19 According to the “two-hit” hypothesis, additional cooperating mutations are needed to generate the malignant founding clone in AML.11


The past 2 decades have witnessed dramatic changes in the way in which AML is classified; the classification is now based on identifying the genetic abnormalities present in an individual patient’s disease.20,21 In 1999, the World Health Organization (WHO) developed a system to classify AML that incorporated the information known at the time about cytogenetic abnormalities.22 Subtypes in the WHO classification are based on morphology, immunophenotype, and molecular/genetic features. Specific gene mutations were added to the classification system in the 4th edition, published in 2008, where “AML with recurrent genetic abnormalities” was further divided into subgroups based on the presence of translocations, gene fusions, or single molecular mutations.23 An updated revision of the 4th edition was published in 2016.24 Specific AML disease entities continued to be identified by focusing on significant cytogenetic and molecular genetic subgroups, incorporating new data from the previous 8 years that have important diagnostic, prognostic, and therapeutic implications (Table 1).24 The molecular basis of inv(3)(q21.3q26.2) or t(3;3)(q21.3;q26.2) is now defined as a rearrangement of GATA2 with MECOM; “AML with NPM1 mutation” and “AML with CEBPA mutation” became entities; “AML with CEBPA mutation” is now restricted to biallelic (and not monoallelic) mutation; and “AML with RUNX1 mutation” and “AML with BCR-ABL1 gene fusion” were added as provisional entities.24,25

AML Genomic Landscape

Many factors, including age, fitness, cytogenetics, and molecular analysis, are taken into consideration when developing a treatment strategy for patients with AML. The combination of cytogenetic information provided by karyotype analysis and the identification of molecular abnormalities is crucial to the management of patients with the disease, as it provides invaluable prognostic information regarding remission rates, relapse risk, and overall survival (OS) outcomes.20,26,27

Cytogenetics and Gene Alterations

As discussed, AML is a heterogeneous disease characterized by a high degree of recurrent genetic alterations. In addition to their importance when subclassifying AML, cytogenetic analysis and mutation status are useful for predicting prognosis, and may help guide treatment strategies.26,28 It is important to note that the prognostic impact of many markers is context-dependent. Gene-gene interactions occur, with the effect of a given abnormality dependent on the presence and/or absence of another. In 2017, the European LeukemiaNet (ELN) proposed an updated risk stratification system to classify AML as favorable, intermediate, or poor risk based on cytogenetics and molecular aberrations (Table 2).26 The National Comprehensive Cancer Network (NCCN) risk stratification varies only slightly from the risk stratification proposed by the ELN.27

There are several recurrent genetic mutations that have been shown to confer independent prognostic information for patients with AML2. Several of the common mutations are more aggressive and have been linked to poor prognosis, including FMS-like tyrosine kinase 3 (FLT3-ITD), ASXL1, RUNX1, TP53, and KIT (Table 3).25,26

FMS-like tyrosine kinase 3

The FLT3 gene encodes a class III receptor tyrosine kinase. When activated, the FLT3 receptor subsequently activates multiple pathways involved in apoptosis, proliferation, and differentiation of hematopoietic precursor cells in the bone marrow.38-41 Mutated FLT3 is one of the most common gene abnormalities in AML; it is mutated in approximately one-third of newly diagnosed cases, the majority of which are cytogenetically normal (CN) AML.28,42 Two major classes of activating mutations can occur within FLT3: those with internal tandem duplications (ITD) and those with point mutations in the tyrosine kinase domain (TKD).28,42 FLT3-ITD mutations, which are more prevalent than FLT3-TKD mutations, are detected in approximately 25% of adult patients newly diagnosed with AML, compared with FLT3-TKD mutations, which are detected in approximately 7% of patients with AML.28,42 In addition to CN-AML, FLT3-ITD mutations are frequently associated with t(6;9)(p23;q34), as well as with t(15;17)(q22;q12) in acute promyelocytic leukemia.43

Both FLT3-ITD and FLT3-TKD mutations lead to constitutive, ligand-independent activation of the FLT3 receptor, dysregulation of downstream pathways, and, subsequently, inhibition of apoptosis and differentiation, and promotion of proliferation.44 Although the evidence behind the prognostic value of FLT3-TKD is mixed, numerous studies have demonstrated the negative prognostic influence of FLT3-ITD. Whereas some studies show an association between FLT3-TKD mutations and poor prognosis, others show no prognostic impact or favorable outcomes associated with FLT3-TKD mutations.27,28

FLT3-ITD at Diagnosis

Patients with AML harboring an FLT3-ITD mutation typically have a significant disease burden presenting as leukocytosis, with high infiltration of bone marrow.42 Numerous studies have reported the presence of FLT3-ITD mutations as an independent predictor of higher relapse rate, shorter remission duration, and poorer OS.42,45-47 Several studies suggest that the prognostic implications of FLT3-ITD depend on the allelic ratio of FLT3-ITD to wild-type (WT) FLT3.26 Patients with FLT3-ITDhigh have a particularly poor prognosis.48

FLT3-ITD and Hematopoietic Stem Cell Transplant

For some patients with intermediate-risk or poor-risk AML, the best hope for long-term survival may be hematopoietic stem cell transplant (HSCT). In newly diagnosed patients with an FLT3-ITD mutation, HSCT has been associated with longer OS compared with patients who either did not complete HSCT or received chemotherapy.49-51 Allogeneic-HSCT (allo-HSCT) in the first complete remission (CR1) is generally recommended in FLT3-ITD–positive AML.52,53 The role of allo-HSCT in CR1 was also evaluated in a retrospective subgroup analysis of 209 patients with intermediate-risk FTL3-ITD–positive AML.54 Patients with FLT3-ITDhigh (allelic ratio >0.8) and patients with FLT3-ITDlow (allelic ratio ≤0.8) and WT-NPM1 had improvements in OS and event-free survival (EFS) with allo-HSCT as compared with consolidation chemotherapy.

As discussed, the 2017 ELN recommendations for the diagnosis and management of AML in adults included a prognostic classification.26 NPM1 mutated AML with FLT3-ITDlow is included in the favorable prognosis category, and thus, allo-HSCT in CR1 is not actively recommended for those patients.26,55 Most studies suggest that patients with an NPM1 mutation and FLT3-ITDlow have similar, favorable outcomes compared with patients with an NPM1 mutation but no FLT3-ITD. AML with WT-NPM1 and FLT3-ITDhigh has a poor prognosis.26 However, one retrospective study of 147 patients with FLT3-ITD–positive AML demonstrated that patients with a low allelic ratio (<0.5) and a concurrent NPM1 mutation who underwent allo-HSCT in CR1 had higher rates of relapse-free survival (RFS) and OS than those who did not.55 Multivariate analysis identified allo-HSCT in CR1 as the sole favorable prognostic factor.

FLT3-ITD in Relapsed/Refractory AML

In first relapse, patients with FLT3-ITD mutations have even poorer prognosis, with median survival from relapse reported in one study as 13 weeks, despite salvage therapy.56 In patients with relapsed AML, the presence of the FLT3-ITD mutation is associated with significantly worse OS compared with FLT3-WT disease.56 In a retrospective study of 138 patients with relapsed/refractory AML receiving salvage therapy, a multivariate analysis demonstrated that disease status (relapse <12 months, including refractory patients), FLT3-ITD–positive status, and high-risk cytogenetics were the 3 strongest independent adverse prognostic factors for OS and EFS.57

FLT3-ITD and the Elderly Patient

AML in the elderly is characterized by a distinct genetic and epigenetic landscape. Within defined cytogenetic risk groups, elderly patients with the disease have higher relapse rates and show inferior outcomes compared with younger patients of the same risk group.58,59 It is unclear whether the spectrum and prognostic relevance of gene mutations are similar between younger and older patients with AML.60

AML is most frequently diagnosed among patients aged 65 to 74 years.4 As discussed, for patients with FLT3-ITD–positive AML in CR1, evidence from several retrospective analyses suggests that allo-HSCT can provide survival benefit.61,62 The majority of studies supporting this strategy have been performed in young patients. However, one retrospective study assessed the role of allo-HSCT in 291 patients aged ≥60 years with intermediate-risk FLT3-ITD positive AML.62 Most patients (82%) in this study received reduced-intensity conditioning. The 2-year leukemia-free survival rate was 56% for patients receiving transplant in first remission, 22% in second remission, and 10% in patients with active disease. Nonrelapse mortality for the entire cohort was 20%. However, not all elderly patients may be suitable candidates for allo-HSCT. Patients of advanced age and/or those who are deemed unsuitable for intensive chemotherapy may have lower tolerance to cytotoxic agents, further limiting treatment options. These patients may be candidates for therapies that are less intensive, which may include targeted agents, low-intensity chemotherapy, and agents being evaluated in clinical trials.63

The Importance of Timely Testing Across the Care Continuum

Current literature shows that FLT3 mutation status may be unstable during disease progression in AML. FLT3 mutations that were not originally detected at diagnosis can appear at relapse and may affect prognosis.64

At Diagnosis

For fit patients with newly diagnosed AML, the goal of induction chemotherapy is to achieve complete response, thereby enabling them to progress to consolidation therapy.2 The frontline management of patients with AML is rapidly changing, and prompt genetic analysis has become necessary for identifying cytogenetic and molecular changes that can inform the selection of appropriate induction therapy.

FLT3-ITD mutations are concurrently present in approximately 40% of AML cases with an NPM1 mutation. The presence of the FLT3-ITD mutation can confer an adverse prognosis for those with favorable NPM1 mutations.20,53 In addition, the favorable prognostic impact of biallelic-mutated CEBPA is mitigated in the presence of FLT3-ITD mutations.65 Interpretation of genetic abnormalities must be performed in the context of one another.

The detection of FLT3-ITD mutations at diagnosis is recommended as part of routine clinical practice and may provide prognostic information and treatment guidance for patients with AML.66 The 2017 ELN recommendations for the diagnosis and management of AML in adults advise that the diagnostic workup should include screening for mutations in FLT3.26 The guideline recommends testing for the presence of FLT3-ITD and FLT3-TKD mutations, as well as for determining the allelic ratio of FLT3-ITD to FLT3-WT. The NCCN includes molecular analyses for FLT3 (ITD and TKD) as part of their guidelines for evaluating patients for AML.27 A joint guidance from the College of American Pathologists (CAP) and the American Society of Hematology (ASH) for the initial diagnostic workup of acute leukemia was also published in 2017.67 The CAP-ASH guidelines make a “strong recommendation” that “[f]or pediatric and adult patients with suspected or confirmed acute myeloid leukemia (AML) of any type, the pathologist or treating clinician should ensure that testing for FLT3-ITD is performed.”

Consolidation Therapy

The goal of consolidation therapy, which may include chemotherapy and/or HSCT, is to eliminate any residual, undetectable disease and achieve long-term disease-free survival.2,27 In 2017, the ELN proposed that minimal residual disease (MRD) should be monitored following both induction and consolidation therapy to assess remission status and the kinetics of disease response, and after consolidation to detect impending relapse.26 Monitoring should include a panel of molecular mutations, including FLT3-ITD, NPM1, CEBPA, TP53, ASXL1, and RUNX1.26,68 However, the 2018 NCCN guidelines do not provide recommendations on the use of MRD monitoring.27 Standardized methodologies for measuring MRD are not well defined or widely available, and additional research is needed to select markers that are reliable indicators of clinical relapse.

At Relapse and Beyond

Following induction and consolidation therapy, clonal evolution may result in changes in FLT3-ITD mutation status in patients with relapsed/refractory disease.64,69 In a single-center retrospective analysis of 3555 patients with AML, a subgroup analysis of 680 patients with FLT3 mutations found that >6% had a change in FLT3 status between diagnosis and relapse. Gains of FLT3 mutation occurred 6 times more frequently than losses.64 Evidence also suggests that the prognostic impact of FLT3-ITD is not limited to newly diagnosed AML. The presence of FLT3-ITD may have an adverse effect on response in the setting of relapse and has been associated with shorter survival after relapse.56

Mutation status should be a key consideration in the treatment strategy for patients with AML. Molecular analysis can identify recurring gene fusions and acquired somatic mutations, with prognostic value that may inform treatment pathways.56,64,69 Because of the potential for clonal evolution of AML, the mutations present at relapse may differ from those present at initial diagnosis. Therefore, timely molecular testing is not only crucial at diagnosis but is also an important consideration at relapse.

Diagnostic Methods and Techniques

The use of a rapid and reproducible molecular diagnostic assay has the potential to identify patients with AML who have a poor prognosis and allow for early intervention with appropriate therapies.26,42,70,71 Available diagnostic methods and techniques, including quantitative polymerase chain reaction (PCR) and next-generation sequencing (NGS), may vary in important characteristics, including sensitivity and ease of use (Table 4). Diagnostic assays also have the potential to allow for early detection of relapsed disease following treatment.

PCR assays have high specificity and varying sensitivity for detection of molecular mutations.71 In addition, although the clinical impact of detecting residual FLT3-ITD quantitatively is unknown, quantitative PCR methods have the potential to be used for monitoring disease progression after induction, consolidation, and salvage therapy.26,75 NGS methods such as whole-genome sequencing, whole-exome sequencing, and multiplex-targeted NGS, although often having lower sensitivity than PCR, can sequence thousands of genes at one time, offering the ability to detect novel or rare genes/variants (also called discovery power). However, NGS may require the analysis of large volumes of data, which may limit its utility in the clinical setting.71

Unmet Needs and Challenges

After more than 30 years with limited advances in treatment, novel formulations and therapies are emerging that may provide new options for patients with AML. However, more therapeutic choices and further advances in understanding the biology of AML are still needed.

Current challenges include:

  • Timely molecular testing: Because genetic testing is no longer purely prognostic, fast processing is important at both diagnosis and relapse to ensure prompt identification of the most appropriate treatment pathway for individual patients.
  • Improved transplant rates: For some patients with intermediate-risk or poor-risk AML, the best hope for long-term survival may be HSCT, as it is associated with significant improvement in OS and RFS.
  • Effective and tolerable therapies: Elderly and/or frail patients, as well as patients who may not be able to tolerate intensive salvage chemotherapy, do not have many effective treatment options.26,63 These patients may be candidates for therapies that are less intensive.


Some mutations, including FLT3-ITD, are associated with poor prognosis. Mutation status should be a key consideration in treatment strategies; thus, timely molecular testing is crucial at diagnosis. In addition, the mutations present at relapse may differ from those present at initial diagnosis. Therefore, it may be important to perform genetic testing not only at diagnosis, but at multiple times across the care continuum for patients with AML.


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