Acute Myeloid Leukemia Genetics

Updated: Mar 02, 2023
  • Author: Ari VanderWalde, MD, MPH, MA, FACP; Chief Editor: Karl S Roth, MD  more...
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Practice Essentials

Acute myeloid leukemia (AML) is a heterogeneous malignancy that most commonly affects persons who are 60 years of age and older. The diagnosis, prognosis, and treatment of acute myeloid leukemia (AML) has been transformed from a disease defined, classed, and staged based on histologic characteristics alone to a disease classified largely based on genetic, genomic, and molecular characteristics. Patients with AML can be stratified according to risk: favorable, intermediate, or adverse. The World Health Organization (WHO) classifies AML by a number of factors, including clinical history, cytogenetic results, molecular genetics, morphology, and immunophenotype. [1, 2, 3] Cytogenetic analysis of AML has become essential for disease diagnosis, classification, prognostic stratification, and treatment guidance. Molecular genetic analysis of CEBPA, NPM1, and FLT3 is already standard of care in patients with AML, and mutations in several additional genes are assuming increasing importance. [2, 4, 5, 6, 7]

Genetic mutations (eg, NPM1, FLT3, CEBPA, TET-2, c-KIT, DNMT3A, IDH, RUNX1, AXSL1, WT1, Ras gene mutations) serve as important prognostic markers and potential therapeutic targets. [2]

The risk pattern in AML is determined not only by cytogenetic abnormalities, such as chromosomal deletions, duplications, or substitutions, but also by the elucidation of certain molecular mutations leading to overexpression or underexpression of one of many proteins.

Cytogenetic studies performed on bone marrow in patients with AML play a crucial role in characterizing the leukemia, helping determine disease aggressiveness, response to treatment, and prognosis. [8] For example, the finding of a translocation between chromosomes 15 and 17, or t(15;17), is associated with a diagnosis of acute promyelocytic leukemia (APL), a subtype of AML that is treated and monitored differently from other subtypes. [9]

The French-American-British (FAB) classification and the World Health Organization (WHO) classification use a variety of factors to classify AML as poor-risk, intermediate-risk, and better-risk disease. In general, better-risk disease is associated with long-term survival of up to 65%, medium-risk disease is associated with long-term survival of about 25%, and poor-risk disease is associated with long-term survival of less than 10%. [2, 10, 1]

Cytogenetic abnormalities associated with disease risk are shown in the Table, below. [11, 12, 13]

Table. Cytogenetic Risk Factors (Open Table in a new window)

Risk Group

Cytogenetic Abnormality

Better Risk

inv(16), t(16;16), t(8;21), t(15;17)

Intermediate Risk

Normal cytogenetics, +8, t(9;11); other chromosomal abnormalities

Poor Risk

-5, 5q-, -7, 7q-, 11q23 other than t(9;11), inv(3), t(3;3), t(6;9),

t(9;22), complex findings (≥3 clonal chromosomal abnormalities)

In addition to cytogenetic abnormalities, several molecular abnormalities have been shown to have prognostic importance in patients with AML.

FLT3 is the most commonly mutated gene in AML and appears to be activated in one third of AML cases. Internal tandem duplications (ITDs) in the juxtamembrane domain of FLT3 are seen in 25% of AML cases, while others show mutations in the activation loop of FLT3. Patients with FLT3 -ITD tend to have a poor prognosis, and in a patient with normal cytogenetics (otherwise intermediate risk), the presence of FLT3 -ITD mutation changes the patient to poor risk. [14, 12, 15, 16, 17, 18, 19, 20]

Mutation in NPM1 is generally favorable; patients with this mutation show increased response to chemotherapy and improved survival (changes otherwise intermediate-risk patients into better-risk). However, if present together with the FLT3 mutation, this survival benefit is negated. [21] Mutations in CEBPA are detected in 15% of patients with normal cytogenetics and are associated with a longer remission duration and longer overall survival. [22] Of note, the presence of c-KIT mutations in patients with otherwise favorable cytogenetic markers [eg, t(8:21), inv(16)] confers a higher risk of relapse and would place an otherwise better-risk patient into the intermediate-risk category. [12, 23]

Other molecular markers, such as IDH1, IDH2, and DNMT3A, have been suggested to be predictive of risk and response to treatment. However, the relationship between these markers and risk of relapse/death has not been fully elucidated, and tests for these markers are not routinely available. As such, they are not typically included in genetic/molecular risk classification schema. [12]


Clinical Implications

Testing for key genetic markers in patients with AML is important for both prognostic and treatment purposes. Generally, the relatively slow turnaround time for cytogenetic and molecular testing makes it difficult to tailor the initial induction based on these factors. However, the choice of consolidation and/or maintenance therapy can often benefit from risk stratification using genetic information. Treatment decisions have been made using this information in one of two ways: in deciding on the aggressiveness of treatment, and in determining whether targeted therapy may influence the genetic or genomic aberration and specifically treat the individual’s tumor.

A classic example of the latter is seen in patients with APL. Its characteristic t(15:17) translocation leads to production of an abnormal fusion protein known as PML-RAR alpha. In normal leukocytes, the RAR protein interacts with retinoic acid to promote cellular differentiation. However, the fusion gene product between the chromosomes in patients with APL causes the retinoic acid receptor to bind more tightly to the nuclear corepressor factor. This prevents the gene from being activated with physiologic doses of retinoic acid, and differentiation from promyelocytes into leukocytes does not occur, leading to a clonal overgrowth of promyelocytes. [9]

The discovery that supraphysiologic doses of all-trans retinoic acid (ATRA) can overcome PML-RAR alpha blockade of the retinoic acid receptor led to the use of ATRA in combination with chemotherapy in patients with APL, which yields very high rates of long-term survival. [9]

Tailoring conventional therapy to risk level, rather than targeting single mutations, is slightly more complicated and subjective. As in all diseases, the decision of which agents to use in AML depends on many factors, including functional status and age of the patient; determination of whether the cancer is secondary to previous cancer therapy or is an abnormal clone secondary to other hematologic disorders such as myelodysplastic syndrome; and the agents and resources available to the treating physician.

Patients with favorable-risk disease [ie, those with t(8;21) or inv(16)] tend to have low relapse rates following consolidation with high-dose cytarabine. Autologous or allogeneic stem cell transplants in these situations should be reserved for patients who have relapsed disease. [12]

Patients with poor-risk disease are rarely cured with chemotherapy alone and should be offered allogeneic transplantation in first remission and/or enrolled in a clinical trial. This includes patients who have intermediate-risk disease by cytogenetics but high-risk disease by molecular diagnostics, such as FLT3 -ITD. These patients also are at high risk for a relapse following transplantation, but transplant offers them the best chance of long-term remission. In an EORTC/GIMEMA trial, these poor-risk patients underwent matched-sibling stem cell transplant and had up to 43% 4-year disease-free survival. [24]

Midostaurin (Rydapt), a multikinase inhibitor, received approval for adults with newly diagnosed AML who are FLT3 mutation-positive, as detected by an FDA-approved test. The companion test, LeukoStrat CDx FLT3 Mutation Assay, was also approved. Midostaurin in combination with standard cytarabine and daunorubicin induction and cytarabine consolidation chemotherapy experienced a 23% improvement in overall survival (P = 0.0074) compared to those treated with standard induction and consolidation chemotherapy alone. [25, 26, 14]

Gilteritinib was approved for adults with AML with an FLT3 mutation who have have had a relapse or have been refractory to treatment. FDA approval was based on interim analysis of the ongoing ADMIRAL clinical trial, a phase 3 open-label, multicenter, randomized study comparing gilteritinib with salvage chemotherapy. Salvage chemotherapy consisted of low-dose cytarabine or azacitidine, or MEC (mitoxantrone, etoposide, and intermediate-dose cytarabine) or FLAG-IDA (fludarabine, cytarabine, G-CSF, and idarubicin). [27]

The choice of treatment for patients with intermediate-risk disease is controversial. While some oncologists refer intermediate-risk patients in first remission for transplant, others give standard consolidation with high-dose cytarabine and only refer patients for transplant if they relapse. Neither option has yet been found categorically to be preferable. [12]

Studies focusing on molecular markers such as FLT3 -ITD,NPM1, CEBPA, IDH1, IDH2, and DNMT3A are helping to define which patients with intermediate-risk disease by cytogenetics should receive standard consolidation therapy versus transplantation. The National Comprehensive Cancer Network (NCCN) currently recommends routine evaluation for CEBPA, NPM1, and FLT3 -ITD in patients with normal cytogenetics, as well as testing for c-KIT in patients with otherwise favorable cytogenetics such as inv(16) or t(8;21). [12, 28]

Small-molecule mutant IDH selective inhibitors are a class of targeted IDH inhibitors that bind within the mutant IDH1 and/or IDH2 catalytic active site, preventing the oncogenic reduction reaction of αKG to the oncometabolite D-2HG. Early clinical studies have demonstrated evidence of clinical activity via myeloid maturation. A unique side effect of targeted IDH therapy, termed “IDH differentiation syndrome,” consisting of nonspecific clinical symptoms including culture-negative fever, edema, hypotension, and pleural and/or pericardial effusions, often in the setting of neutrophil-predominant leukocytosis, has been described in approximately 5 to 10% of patients across IDH inhibitor clinical trials. [29]

The NCI/COG TARGET-AML initiative study demonstrated significant variability in the mutational profile and clonal evolution of pediatric AML from diagnosis to relapse. Mutations that persisted from diagnosis to relapse had a significantly higher diagnostic variant allele fraction (VAF) than those that resolved at relapse (median VAF 0.43 vs. 0.24, P< 0.001). Further analysis revealed that 90% of the diagnostic variants with VAF greater than 0.4 persisted to relapse, as compared to 28% with VAF less than 0.2 (P< 0.001). [28]


Genetic Testing

Cytogenetic testing of bone marrow samples is widely commercially available, and results are consistent and interpretable. Fluorescence in-situ hybridization (FISH) can also identify cytogenetic abnormalities and should be done in addition to (but not instead of) routine cytogenetics.

In April 2017, the FDA approved LeukoStrat CDx FLT3 Mutation Assay. The presence of the FLT3 mutation identifies patients who are considered poor-risk and are therefore likely to benefit from treatments other than conventional chemotherapy (eg, midostaurin, transplant). Midostaurin, a multikinase inhibitor, was also approved by the FDA in April 2017. It is indicated in combination with standard cytarabine and daunorubicin induction and cytarabine consolidation chemotherapy for adults with newly diagnosed AML who are FLT3 mutation-positive, as detected by an FDA-approved test.

Analyses of other molecular markers such as NPM1, c-KIT, and CEBPA are less commonly available outside research institutions. If a physician is in an area where these tests are not readily available, it is recommended to preserve additional aliquots of bone marrow aspirate at the time of diagnosis. [12]  Once cytogenetic information is returned, the decision can be made whether molecular markers would further contribute to treatment decisions. For example, if the local pathology laboratory shows normal cytogenetics, it would be of use to send the additional aliquots to an outside research or academic facility to test further for mutations of biomarkers.