Acute Myeloid Leukemia Mutation Panel by Next Generation Sequencing

Content Review: August 2023 Last Update: October 2023

For more information on ARUP’s myeloid malignancies panel, which test the genes in this panel and additional genes relevant to other myeloid malignancies, refer to the Myeloid Malignancies Mutation and Copy Number Variation Panel by Next Generation Sequencing Test Fact Sheet.

For information on other ARUP tests relevant to AML, including information on single-gene tests, refer to the Acute Myeloid Leukemia Molecular Genetic Testing Test Fact Sheet.

For more information on ARUP’s genomic microarray testing in oncology, refer to the Cytogenomic Microarray - Oncology Test Fact Sheet.

Acute myeloid leukemia (AML) is a myeloid malignancy (ie, a clonal disorder of hematopoietic stem and progenitor cells). Recent studies have identified recurrently mutated genes with diagnostic and/or prognostic significance in AML. The presence of certain variants may inform clinical management.

This multigene panel by massively parallel sequencing (MPS; also referred to as next generation sequencing [NGS]) detects molecular changes including single nucleotide variants (SNVs), small insertions and deletions (indels) relevant to AML. This test is more cost effective than the use of multiple single gene tests and can be used to complement the morphologic and cytogenetic workup of AML.

Disease Overview

Diagnostic, Prognostic, and Treatment Issues

Identification of one or more clonal genetic abnormalities, variants, or patterns of variants in patients with AML may:

  • Aid in establishing the diagnosis and subclassification
  • Aid in determination of prognosis
  • Inform clinical management

Genetics

Genes Tested

ANKRD26, ASXL1, CEBPA, DDX41, DNMT3A, ETV6, FLT3, GATA2, IDH1, IDH2, KIT, KRAS, NPM1, NRAS, RUNX1, TP53, WT1

For some genes, one or more exons of the preferred transcript are not covered by sequencing for the indicated gene. Refer to the Genes Tested table below for full list of targeted regions and exclusions.

Test Interpretation

Results

Reported variants are classified into two categories:

  • Tier 1: Mutations with known clinical significance in hematologic malignancies
  • Tier 2: Variants of unknown clinical significance in hematologic malignancies

Limitations

Limit of Detection

  • SNVs and small variants <24 base pair (bp): 5% variant allele fraction (VAF)
  • Variants >24 bp: may be detected at limit of detection (LOD), but analytic sensitivity may be reduced

Variants That Will Not Be Detected

  • Variants in regions that are not included in the preferred transcript for the targeted genes
    • Refer to the Genes Tested table below for full list of targeted regions and exclusions.
  • Copy number variants (losses or gains)
  • Loss of heterozygosity
  • RNA variants
  • Gene fusions, balanced translocations, and other structural variants

Some variants may not be identified due to technical limitations in the presence of pseudogenes or in repetitive or homologous regions.

Variants That Will Not Be Reported

Benign or likely benign variants in the preferred transcript

Additional Limitations

  • This test is not intended to detect minimal residual disease (MRD).
  • Interpretation of this test result may be impacted if this patient has had an undisclosed allogeneic bone marrow transplant or stem cell transplant.
  • This test does not distinguish between somatic and germline variants.

Analytic Sensitivity

Variant Class Analytic Sensitivity (PPA)a Estimate (%) Analytic Sensitivity (PPA) 95% Credibility Regiona (%)

SNVs

96.9

95.1-98.1

Insertions/duplications (1-24 bp)

98.1

95.5-99.3

Insertions/duplications (>24 bp)

>99

92.9-100.0

Deletions (1-24 bp)

96.7

92.8-98.7

Deletions (>24 bp)

90

79.5-96.1

MNVs

97

93.0-99.0

FLT3 ITDs

>99

97.1-100.0

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived.

bp, base pairs; ITDs, internal tandem duplications; MNVs, multinucleotide variants; PPA, positive percent agreement

Genes Tested

Genes Tested by Acute Myeloid Leukemia Mutation Panel by Next Generation Sequencing
Gene Preferred Transcripta Excluded Exonsb

ANKRD26

NM_014915

ASXL1

NM_015338

CEBPA

NM_004364

DDX41

NM_016222

DNMT3A

NM_175629

ETV6

NM_001987

FLT3

NM_004119

GATA2

NM_032638

IDH1

NM_005896

IDH2

NM_002168

KIT

NM_000222

KRAS

NM_004985

NPM1

NM_002520

1

NRAS

NM_002524

RUNX1

NM_001754

TP53

NM_000546

WT1

NM_024426

aThis is the transcript number used for analyzing and reporting variants. The transcript version number may change periodically and thus is not listed here. The transcript with version number will be included on the patient's report if a variant is detected in the gene.

bNoncoding exons are not analyzed, except for regions containing known clinically relevant variants in the ANKRD26 5’UTR. In addition, coding exons noted here are not sequenced due to technical limitations of the assay.