Streamline MPN Genomic Profiling with Oncomine Myeloid Assay GX v2

Myeloproliferative neoplasms (MPNs) are a group of disorders identified by an overproduction of cells derived from a myeloid lineage.1 These disorders are divided into two broad categories: BCR::ABL1-positive MPNs, consisting of chronic myeloid leukemia (CML), and BCR::ABL1-negative MPNs, including polycythemia vera (PV), essential thrombocythemia (ET), primary myelofibrosis (PMF), chronic neutrophilic leukemia (CNL), chronic eosinophilic leukemia (CEL), among other subtypes.

 

Research on MPN genomic profiling often uses single gene evaluation methods to detect driver mutations in JAK2, MPL, and CALR. This approach can be time-consuming and labor-intensive, typically requiring multiple technologies (e.g., polymerase chain reaction (PCR), Sanger sequencing, and next-generation sequencing (NGS)) to achieve a comprehensive genomic profile for MPNs. Initiating MPN research with a targeted NGS panel can provide a more complete, faster, and efficient genomic profile.2

Streamline MPN profiling with Oncomine Myeloid Assay GX v2

Integrate MPN samples into the myeloid NGS run using the Ion Torrent Oncomine Myeloid Assay GX v2 on the Genexus System for a comprehensive myeloid solution. This assay analyzes 45 DNA target genes and 34 RNA fusion driver genes, sequencing over 800 unique fusion transcripts, and delivers a detailed mutational report in as little as 24 hours. It covers relevant targets for major myeloid malignancies, including AML, MDS, MPN, and MDS/MPN neoplasms (Table 1).

Oncomine Myeloid Assay GX v2 gene list (MPN-related genes are bolded*) 

HotSpot genes (28) Full genes (17) Fusion driver genes (34) Expression genes (5) Expression control genes (5)
ANKRD26 IDH1 PPM1D ASXL1 RB1 ABL1 HMGA2 NUP98 BAALC  EIF2B1 
ABL1 IDH2 PTPN11 BCOR RUNX1 ABL2 JAK2 NUP214 MECOM  FBXW2 
BRAF JAK2 SMC1A CALR SH2B3 BCL2 KAT6A (MOZ) PAX5 MYC  PSMB2 
CBL KIT SMC3 CEBPA STAG2 BRAF KAT6B PDGFRA SMC1A PUM1 
CSF3R KRAS SETBP1 ETV6 TET2 CCND1 KMT2A (includes PTD) PDGFRB WT1 TRIM27
DDX41 MPL SF3B1 EZH2 TP53 CREBBP MECOM RARA    
DNMT3A MYD88 SRSF2 IKZF1 ZRSR2 EGFR MET RUNX1    
FLT3 (ITD, TKD) NPM1 U2AF1 NF1   ETV6 MLLT10 TCF3    
GATA2 NRAS WT1 PHF6   FGFR1 MRTFA (MKL1) TFE3    
HRAS     PRPF8   FGFR2 MYBL1 ZNF384    
          FUS MYH11      
            NTRK2      
            NTRK3      

*This table includes MPN and CML-related genes, as well as select fusion drivers interrogated to clarify CEL research.

Why utilize Oncomine Myeloid Assay GX v2 for MPN genomic profiling?

Detect driver mutations—identify driver mutations in genes such as JAK2, MPL, and CALR, found in around 90% of MPNs, for a more complete coverage of critical variants

 

Examine additional MPN-contributing mutations—investigate additional mutations contributing to MPNs, including ASXL1, EZH2, TET2, IDH1, IDH2, SRSF2, and SF3B1, as highlighted in recent research3​

 

Identify fusion genes—discover key fusion genes such as BCR::ABL in CML and fusions involving PDGFRA, PDGFRB, and FGFR1, supporting research and distinction between chronic eosinophilic leukemia (CEL) and myeloid/lymphoid neoplasms with eosinophilia4

 

Profile MDS/MPN neoplasms—obtain detailed genomic profiling of myelodysplastic/myeloproliferative (MDS/MPN) neoplasms, rare myeloid neoplasms with both proliferative and dysplastic features5

A rapid and automated NGS workflow from sample to report

Start with any common myeloid sample type, including whole blood, bone marrow, or peripheral blood leukocytes. From there, the Genexus System integrates and automates nucleic acid extraction, purification, quantification, library preparation, sequencing, analysis and reporting within a single software ecosystem.

  • Whole blood
  • Peripheral blood leukocytes (PBLs)
  • Bone marrow
  • Nucleic acid extraction and quantification
  • Library preparation
  • Sequencing
  • Reporting & analysis
  • Biomarkers linked to relevant evidence from public data sources

Expanded utility of the Genexus System

Integrating MPN samples into the Oncomine Myeloid Assay GX v2 on the Genexus System enhances the instrument's versatility and minimizes the necessity for batching, allowing for more efficient and timely analysis.

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References

1. Grabek J, Straube J, Bywater M, Lane SW. MPN: The Molecular Drivers of Disease Initiation, Progression and Transformation and their Effect on Treatment. Cells. 2020 Aug 14;9(8):1901. doi: 10.3390/cells9081901. PMID: 32823933; PMCID: PMC7465511

2. Kuo FC, Mar BG, Lindsley RC, Linderman NI. The relative utilities of genome-wide, gene-panel, and individual gene sequencing in clinical practice. Blood. 2017;130(4):433-439.

3. Damien Luque Paz, Robert Kralovics, Radek C. Skoda. Genetic basis and molecular profiling in myeloproliferative neoplasms. Blood (2023) 141 (16): 1909-1921. https://doi.org/10.1182/blood.2022017578

4. Andreas Reiter, Jason Gotlib. Myeloid neoplasms with eosinophilia. Blood (2017) 129 (6): 704–714. https://doi.org/10.1182/blood-2016-10-695973

5. Pati H, Kundil Veetil K. Myelodysplastic Syndrome/Myeloproliferative Neoplasm (MDS/MPN) Overlap Syndromes: Molecular Pathogenetic Mechanisms and Their Implications. Indian J Hematol Blood Transfus. 2019 Jan;35(1):3-11. doi: 10.1007/s12288-019-01084-y. Epub 2019 Jan 24. PMID: 30828140; PMCID: PMC6369066.

6. Grinfeld J, Nangalia J, Baxter EJ, Wedge DC, Angelopoulos N, Cantrill R, Godfrey AL, Papaemmanuil E, Gundem G, MacLean C, Cook J, O'Neil L, O'Meara S, Teague JW, Butler AP, Massie CE, Williams N, Nice FL, Andersen CL, Hasselbalch HC, Guglielmelli P, McMullin MF, Vannucchi AM, Harrison CN, Gerstung M, Green AR, Campbell PJ. Classification and Personalized Prognosis in Myeloproliferative Neoplasms. N Engl J Med. 2018 Oct 11;379(15):1416-1430. doi: 10.1056/NEJMoa1716614. PMID: 30304655; PMCID: PMC7030948

For Research Use Only. Not for use in diagnostic procedures.

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