Connect Sign In
FeedbackMassively Parallel Sequencing
Acute myeloid leukemia (AML) is a clonal disorder of hematopoietic progenitor cells. Recent studies have identified recurrently mutated genes with diagnostic, prognostic, and therapeutic significance in AML. The presence of certain variants may inform clinical management.
This multigene panel can be used upon initial diagnosis or overt relapse of AML to assess molecular changes, including single nucleotide variants (SNVs) and small insertions and deletions (indels) in select hotspots of relevant genes via massively parallel sequencing (MPS; also referred to as next generation sequencing [NGS]). This test has a fast turnaround time, which is critical in the timely identification of prognostic markers and advantageous in immediate patient management. In addition, it 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. For testing for subsequent or more comprehensive analyses, refer to the Myeloid Malignancies Mutation and Copy Number Variation Panel by Next Generation Sequencing Test Fact Sheet.
This test is NOT intended to detect minimal residual disease (MRD).
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 of certain subtypes of AML
- Aid in the determination of prognosis and identification of therapeutic targets
- Inform clinical management
Genetics
Genes Tested
| Gene | Transcript (NM) | Covered Exon(s) | Covered Region(s) |
|---|---|---|---|
| CEBPA | NM_004364 | 1 | chr19:33792244-33793320 |
| FLT3 | NM_004119 | 14, 15, 16, 20 | chr13:28608209-28608361 chr13:28608014-28608138 chr13:28602305-28602435 chr13:28592594-28592736 |
| IDH1 | NM_005896 | 4a | chr2:209113083-209113292 |
| IDH2 | NM_002168 | 4 | chr15:90631809-90631984 |
| KIT | NM_000222 | 8, 9, 10, 11, 17 | chr4:55589740-55589874 chr4:55592023-55592226 chr4:55593374-55593500 chr4:55593572-55593718 chr4:55599226-55599368 |
| KRAS | NM_004985 | 2, 3, 4 | chr12:25398198-25398318 chr12:25380158-25380356 chr12:25378538-25378717 |
| NPM1 | NM_002520 | 11a | chr5:170837521-170837569 |
| NRAS | NM_002524 | 2, 3, 4 | chr1:115258661-115258781 chr1:115256411-115256609 chr1:115252180-115252359 |
| TP53 | NM_000546 | All coding (noncoding exon 1 is not covered) | chr17:7579837-7579912 chr17:7579690-7579731 chr17:7579302-7579600 chr17:7578361-7578564 chr17:7578167-7578290 chr17:7577489-7577615 chr17:7577009-7577165 chr17:7576843-7576936 chr17:7573917-7574043 chr17:7572926-7573017 |
| aIndicated exons are partially targeted (for hotspots only) and not reportable in full. | |||
Test Interpretation
Results
Reported variants are classified into two categories:
- Variants with known clinical significance in hematologic malignancies
- Variants of unknown clinical significance in hematologic malignancies
Limitations
Variants Not Detected
- Some variants may not be identified due to technical limitations in the presence of pseudogenes, in GC-rich regions, in repetitive or homologous regions, or in regions overlapping with primers designed for target enrichment.
- Variants at exon-intron boundaries may not be detected.
- Variants in regions that are not included in the targeted coding regions of the preferred transcript for the targeted genes
- Copy number variants (losses or gains)
- Loss of heterozygosity
- RNA variants
- Gene fusions, balanced translocations, and other structural variants
Variants Not Reported
- Benign or likely benign variants in the preferred transcript
- Variants other than hotspot mutations may not be reported
Additional Limitations
- This test is not intended to detect 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
Limit of Detection
- SNVs and small variants <25 base pairs (bp): 5% variant allele fraction (VAF)
- Variants >25 bp: may be detected at limit of detection (LOD), but analytic sensitivity may be reduced
- FLT3 internal tandem duplications (ITDs) (3-126bp): 10% VAF
Analytic Sensitivity
| Variant Class | Analytic Sensitivity (PPA)a Estimate (%) | Analytic Sensitivity (PPA) 95% Credibility Regiona (%) |
|---|---|---|
| SNVs | 98.9 | 95.2-99.8 |
| Insertions/duplications/MNVs (1-25bp) | 100 | 96.2-99.9 |
| FLT3 ITDs | 97.7 | 90.0-99.7 |
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 | ||
For more information on ARUP’s myeloid malignancies panel, which includes 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.