Test Overview
Next-Generation Sequencing and Multiplex Polymerase Chain Reaction (PCR) with Capillary Electrophoresis
This test is intended for the molecular evaluation of myeloid neoplasms, including myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), myelodysplastic/myeloproliferative neoplasms, acute myeloid leukemias (AML), mastocytosis, and myeloid neoplasms with eosinophilia and gene rearrangement. The detection of molecular alterations described in these neoplasms can be useful in their diagnosis and classification. In addition, the pattern of particular alterations can be prognostically informative and can have implications for the use of both targeted and conventional therapies. Given the wide variety of different, clinically significant molecular alterations present in myeloid neoplasms and the importance of the molecular landscape of co-occurring alterations, a next-generation sequencing (NGS) panel-based approach is the optimum method for interrogating these neoplasms. The DNA portion of this NGS panel evaluates 50 genes for substitution and insertion/deletion mutations. RNA is also interrogated for recurrent gene fusions described in myeloid neoplasms and acute leukemia’s, which may not be detected by conventional cytogenetics (cryptic). FLT3 testing is separately ordered, performed using multiplex PCR and capillary electrophoresis, and reported prior to the result for the full NGS panel. While this panel is primarily designed to detect recurrent, somatic molecular alterations described in myeloid neoplasms, germline alterations associated with a genetic predisposition to myeloid neoplasms (e.g. CEBPA, DDX41, RUNX1, ANKRD26, ETV6, GATA2, etc.) can also be detected. This test is intended for diagnostic specimens, not for the detection of minimal residual disease.
Interpretive Report Provided
*Reference ranges may change over time. Please refer to the original patient report when evaluating results.
* Reference ranges may change over time. Please refer to the original patient report when evaluating results.
Some gene mutations associated with myeloid neoplasms can also be detected in individuals with clonal hematopoiesis without evidence of a hematologic malignancy. This test may fail to detect molecular alterations below the limit of detection of this assay (approximately 5% variant frequency for SNV and insertion/deletion mutations and approximately 10% neoplastic cells for gene fusions). Low-level variants may not be detectable in repetitive regions. This test is not intended for the detection of minimal residual disease (MRD). This test will only detect the mutations within the specific gene regions sequenced and the specific gene fusions targeted by this assay (See University of Michigan pathology Handbook for specific information). This assay may fail to detect gene fusions with a low level of expression or with breakpoints not targeted by this assay. This test does not detect gene/exon-level copy number alterations and may not detect large insertion/deletion mutations (> 200 bp). Variant allele frequencies are approximations and may be affected by the percentage of neoplastic cells within the sample, subclonal molecular alterations, concomitant copy number alterations, etc. This test cannot distinguish between somatic and germline alterations without sequencing of germline DNA. Genetic counseling may be necessary for patients in which germline variants are detected. The clinical implications of the findings in this report may change based on evolution of the scientific literature.
Test Details
7-21 days
- AML
- MDS
- MPN
- eosinophilia
- leukemia
- myelodysplastic
- myeloproliferative
- T-LGL
- AITL
- angioimmunoblastic
- TFH
- VEXAS
- ANKRD26
- DDX41
- IDH2
- PHF6
- SRSF2
- ASXL1
- DNMT3A
- JAK2
- PTPN11
- STAG2
- BCOR
- ETNK1
- JAK3
- RAD21
- STAT3
- BCORL1
- ETV6
- KIT
- RHOA
- STAT5B
- BRAF
- EZH2
- KRAS
- RUNX1
- TET2
- CALR
- FLT3
- MAP2K1
- SAMD9
- TP53
- CBL
- GATA1
- MPL
- SAMD9L
- U2AF1
- CEBPA
- GATA2
- NF1
- SETBP1
- UBA1
- CSF3R
- HRAS
- NPM1
- SF3B1
- WT1
- CUX1
- IDH1
- NRAS
- SRP72
- ZRSR2
Specimen Requirements
Collect blood or bone marrow in a lavender top tube. Refrigerate and send intact blood or bone marrow specimen within 48 hours of collection. Fresh tissue (preferably 0.5 cm3, sent in RPMI) and fresh aspirates or body fluids are acceptable. Refrigerate and send, preferably within 24 hours. Frozen tissue specimens – preferably frozen with 1 hour of collection – may also be sent frozen on dry ice. Fresh cell suspensions in RPMI should be refrigerated and sent, preferably within 48 hours. Frozen cell suspensions – preferably frozen with 1 hour of collection – may also be sent frozen on dry ice. Fixed cytogenetic cell suspensions or pellets in Carnoy’s fixative. Refrigerate and send.
Testing of formalin-fixed, paraffin-embedded tissue may be performed if sufficient DNA and RNA can be extracted. A block containing a high percentage of neoplastic cells is preferred. Unstained, UNBAKED slides (5-8, 10-micron slides; 10-15 if few neoplastic cells are present) with associated H&E stained slide are also acceptable. Decalcified tissue or other fixatives will be accepted and the assay attempted; however, these may result in failed testing due to degraded nucleic acid. Both blocks and slides should be stored at room temperature.
Previously extracted DNA and RNA may also be accepted if extracted within a CLIA certified laboratory.
Fibroblast culture from skin biopsy or buccal swab may be acceptable for additional testing intended to differentiate germline and somatic molecular alterations.
Additional Information
Click here for gene regions sequenced for SNV and insertion/deletion variants
Targeted Gene Fusions
Click here for gene fusions detected by this assay
By ordering this test the clinician acknowledges that informed consent has been obtained from the patient as required by applicable state or federal laws and the ordering clinician has authorization from the patient permitting MLabs to report the test results to the ordering clinician. Test includes microdissection billed as a separate additional charge. Test includes pathologist interpretation of results billed as a separate additional charge. This test is not available without interpretation.