Acute Myeloid Leukemia Molecular Genetic Testing

Detect and quantitate gene alterations/translocations/
inversions. Use for minimal residual disease (MRD) and relapse risk monitoring.
CBFB-MYH11 inv(16) Detection, Quantitative 2011114
Method: Reverse Transcription Quantitative Polymerase Chain Reaction
NPM1 Mutation Detection by RT-PCR, Quantitative 3000066
Method: Quantitative Reverse-Transcription Polymerase Chain Reaction
PML-RARA Translocation, t(15;17) by RT-PCR, Quantitative 2002871
Method: Reverse Transcription Polymerase Chain Reaction
RUNX1-RUNX1T1 (AML1-ETO) t(8;21) Detection, Quantitative 2010138
Method: Quantitative Reverse Transcription Polymerase Chain Reaction
Use for diagnosis, prognosis, and management. Not intended for MRD monitoring.
FLT3 ITD and TKD Mutation Detection 3001161
Method: Polymerase Chain Reaction
IDH1 and IDH2 Mutation Analysis, exon 4 2006444
Method: Polymerase Chain Reaction/Sequencing
Use for prognostication of cytogenetically normal AML (CN-AML).
CEBPA Mutation Detection 2004247
Method: Polymerase Chain Reaction/Sequencing
Prognostication in core-binding factor-related (CBF) AML.
KIT Mutations in AML by Fragment Analysis and Sequencing 2002437
Method: Polymerase Chain Reaction/Fragment Analysis/Sequencing
Related Next Generation Sequencing Test

Acute myeloid leukemias (AMLs) are a heterogeneous group of disorders characterized by the clonal expansion of myeloid precursors in the peripheral blood, bone marrow, and/or other tissues, which results in impaired hematopoiesis and bone marrow failure.     AML is the most common acute leukemia in adults (~80% of leukemia cases) and accounts for the largest number of annual deaths from leukemia in the United States.   Gene alterations, along with translocations and inversions, carry prognostic importance in AML. In addition to large chromosomal rearrangements, molecular changes have also been implicated in the development of AML. A comprehensive evaluation of several molecular markers, including FLT3, NPM1, CEBPA, KIT, IDH1, and IDH2, is important for risk assessment and prognostication in certain patients with AML, and may guide treatment decisions. 

For more information on next generation sequencing testing for AML, see Myeloid Malignancies Mutation Panel by Next Generation Sequencing. For information on cytogenetic testing related to AML, see Acute Myeloid Leukemia Panel by FISH, Acute Myeloid Leukemia with Myelodysplastic Syndrome (MDS) or Therapy-Related MDS Panel by FISH and Acute Promyelocytic Leukemia Molecular Testing.

Testing Strategy

At diagnosis, the minimum AML workup includes a bone marrow aspirate for morphology, flow cytometric immunophenotyping, cytogenetics (eg, karyotyping and fluorescence in situ hybridization [FISH]), and appropriate molecular genetic testing.   

Disease Overview

Incidence

>20,0000 cases/year in the U.S. 

Age of Onset

Median is 67 years 

Symptoms

  • Symptoms resulting from thrombocytopenia, neutropenia, and anemia due to the accumulation of blasts in the marrow 
  • Morphologic hallmark: excessive accumulation of blasts (typically >20%) and other defined immature cells which affect one or more myeloid lineage 

Test Interpretation

For more detailed information on the prognostic significance of molecular markers in AML, see the ARUP Consult Acute Myeloid Leukemia topic.

Recurrent Genetic Abnormalities in AML   
Molecular Genetic Alteration Prognostic Significance

CEBPA

Biallelic mutations confer favorable prognosis

FLT3 ITD and TKD

Poor prognosis associated with FLT3 ITD mutation; ​FLT3 TKD mutation has unclear prognosis

IDH1 and IDH2

Unfavorable prognosis; targeted therapy is available for AML with IDH1 or IDH2 mutation

KIT

Poor prognosis, usually associated with core binding factor leukemias; increased risk of relapse

NPM1

Favorable prognosis in patients with normal karyotype and without FLT3 ITD mutation; poor prognosis if present with FLT3 ITD and DNMT3A mutations

CBFB-MYH11a

Usually associated with high rate of complete remission (CR) and long-term, disease-free survival when treated with intensive consolidation therapy

PML-RARAa

More favorable prognosis than any other AML cytogenetic subtype when treated appropriately

RUNX1-RUNX1T1a

Usually associated with a high rate of CR and long-term, disease free survival when treated with intensive consolidation therapy

aThese fusions can initially be screened by FISH, but are also useful in monitoring for MRD.

CR, complete remission

Sources: NCCN, 2019 ; De Kouchkovsky, 2016 ; WHO, 2017 

Sensitivity/Specificity

Gene Methodology Analytical Sensitivity Analytical Specificity

CEBPA

PCR/sequencing

40% mutated cells

100%

FLT3 ITD and TKD

PCR/CE

Signal ratio of 0.05 for ITD and 0.05 for TKD D835

100%

IDH1 and IDH2

PCR/sequencing

40% mutated cells

100%

KIT

PCR/fragment analysis/sequencing

30% mutated cells for exon 17

5% mutated cells for exon 8

100%

NPM1

Quantitative reverse transcription PCR

1:100,000

100%

CBFB-MYH11a

Quantitative reverse transcription PCR )

1:10,000

100%

PML-RARAa

Quantitative reverse transcription PCR

1:10,000

85%

RUNX1-RUNX1T1a

Quantitative reverse transcription PCR

1:100,000

100%

aThese fusions can initially be screened by FISH, but are also useful in monitoring for MRD.

CE, capillary electrophoresis; PCR, polymerase chain reaction

Limitations

  • Variants outside the targeted regions or below the limit of detection will not be identified
  • Results must always be interpreted within the patient's clinical context and in conjunction with other relevant data and should not be used alone for a diagnosis of malignancy
References 
  1. Arber DA, Borowitz MJ, Cessna M, Etzell J, Foucar K, Hasserjian RP, Rizzo D, Theil K, Wang SA, Smith AT, Rumble B, Thomas NE, Vardiman JW. Initial Diagnostic Workup of Acute Leukemia: Guideline From the College of American Pathologists and the American Society of Hematology. Arch Pathol Lab Med. 2017; 141(10): 1342-1393. PubMed
  2. NCCN Clinical Practice Guidelines in Oncology, Acute Myeloid Leukemia. National Comprehensive Cancer Network. Fort Washington, PA [Last update: Mar 2019; Accessed: May 2019]
  3. Weinberg OK, Sohani AR, Bhargava P, Nardi V. Diagnostic work-up of acute myeloid leukemia. Am J Hematol. 2017; 92(3): 317-321. PubMed
  4. De Kouchkovsky I, Abdul-Hay M. 'Acute myeloid leukemia: a comprehensive review and 2016 update'. Blood Cancer J. 2016; 6(7): e441. PubMed
  5. Swerdlow S, Campo E, Jaffe E, Pileri S, Stein H, Thiele J, Arber D, Hasserjian R, Le Beau M. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues, Revised 4th Ed.. Lyon, France: International Agency for Research on Cancer, 2017.

Last Update: October 2019