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Acute myeloid leukaemia (AML) is a group of haematological malignancies which are phenotypically and genetically diverse but for which fusion events are particularly prevalent1. An estimated 30% of patients with AML carry a fusion gene2, and these can aid in classifying the disease subtype helping with diagnosis, prognosis, and deciding treatment strategies3.

Common fusions identified in AML include RUNX1::RUNX1T1, CBFB::MYH11, PML::RARA, as well as KMT2A, NUP98, and MECOM rearrangements4. Fusion events occur as the result of erroneous chromosomal rearrangements or splicing mechanisms, which lead to the joining of two previously independent genes into a single construct. These fusion events, also called gene fusions, can occur in regulatory gene elements that may alter gene expression regulation or cause the constitutive activation of encoded proteins which drives oncogenesis1.


Clinical example of a fusion gene: PML:::RARA

Acute promyelocytic leukaemia is an aggressive subtype of AML, characterised by the presence of the PML::RARA fusion. This fusion arises from the translocation of the retinoic acid receptor alpha (RARA) gene on chromosome seventeen and the promyelocytic leukaemia (PML) gene on chromosome 155, leading to uncontrolled proliferation of myeloid precursor cells6.

Patients who are diagnosed with APL characterized by PML::RARA are typically treated with all-trans-retinoic acid (ATRA) plus chemotherapy or ATRA plus arsenic-trioxide (ATO) which has shown high cure rates6,7. However, RARA can fuse to partners other than PML, albeit in rare cases of AML, with at least fourteen variant translocations identified and these variants may show limited responsiveness to ATRA or ATO therapy8.


World Health Organisation guidelines on AML and fusion events

The World Health Organisation is actively developing updated guidelines on the development and classification of AML4, with a major development being the arrangement of AML into two families: AML defined by differentiation and AML with defining genetic abnormalities.


World Health Organisation variant guidelines

Subtypes of AML captured within genetic abnormalities include those defined by various fusions/rearrangements:

Table of various fusions and rearrangementsTable 1: The SureSeq™  Myeloid Fusion Panel (RUO*) encompasses 18 driver genes covering 30 of the most clinically-relevant fusions for AML, as well as rare or novel variants. Genes highlighted in bold from WHO recommendations are included in the SureSeq™  Myeloid Fusion Panel.


Traditional methods for fusion event detection

Molecular genetic testing can be employed for the detection of fusion events in AML, and beyond. Different approaches to detection include:


Fluorescence in situ hybridisation (FISH)

FISH has been employed in clinical cytogenetics settings and is considered the gold standard for fusion gene identification. Different approaches for FISH can be used, one common method is to utilise two probes each labelled with different fluorophores targeting specific DNA regions of a gene known to be frequently translocated. In the event of a translocation two distinct fluorophore signals will be seen9. Conversely, two common fusion partners can be targeted with two probes each labelled with different fluorophores, in the event of a gene fusion the two fluorophores will be seen to be overlapping9.

While this method benefits from its simplicity and developments over the past years, it can still have limitations. FISH is restricted in the number of fusion genes it can detect simultaneously and the development of validated protocols for the use of FISH probes may be time intensive and require experienced personnel. Additionally, protocols are also typically probe and sample specific and thus could require optimisation for each sample-probe combination.


Reverse transcriptase polymerase chain reaction (RT-PCR)

This method uses reverse transcriptase enzymes to convert RNA into DNA and amplify the subsequent genetic material via PCR. By using specific primers for likely fusion partners, the presence of fusion genes can be detected.

While this method is highly sensitive and often used in disease monitoring it is limited by the number of targets it can detect and cannot identify novel fusion events10.


The potential of RNA-based NGS in detecting fusion events

RNA-based NGS sequencing detects the presence and quantity of RNA and allows for the simultaneous sequencing of multiple regions of interest within a person’s genome. Generally, analysis is performed as:

  • Genetic material is isolated, quantified and fragmented
  • Unique adapters are added for interaction with the sequencer and DNA is amplified
  • DNA is hybridised with specific probes to enrich for targets of interest
  • DNA is pooled and sequenced

Sequencing data can provide information about alternative splicing, mutations, changes in gene expression and importantly fusion events and can generate additional information not obtained through traditional cytogenetic analysis2. Limitations in these existing techniques may also be addressed through NGS panels such as the increased resolution and reduction of analytical burden seen in multi-step testing approaches2.

At OGT we have expanded our existing NGS myeloid portfolio with our SureSeq Myeloid Fusion Panel.*

Intelligently designed in collaboration with leading myeloid cancer experts, the NGS Myeloid Fusion Panel is:

  • Efficient: Simultaneously detect 30+ common fusions
  • Streamlined: Replace multiple technologies with a single assay
  • Expansive: Enhance sample classification with novel/rare fusions

Start your journey with OGT today



Fusion events continue to play a vital role in the molecular landscape of AML and have significant implications in the disease landscape. Detection of these events using advanced technologies, such as targeted RNA sequencing, has been shown to be crucial for accurate classification, risk stratification and targeted treatment of AML patients.

With ongoing advancements in genomic technologies, the understanding of fusion genes in AML is continuously evolving, paving the way for personalised therapies and improved patient outcomes.

Discover more about the NGS SureSeq Myeloid Fusion Panel


  1. Taniue K and Akimitsu N. Fusion Genes and RNAs in Cancer Development. Noncoding RNA. 2021;7:10. doi: 10.3390/ncrna7010010
  2. Thol F. Fusion genes in acute myeloid leukemia: do acute myeloid leukemia diagnostics need to fuse with RNA-sequencing? Haematologica. 2022;107:44–45. doi: 10.3324/haematol.2021.278983
  3. Kerbs P et al. Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements. Haematologica. 2022;107:100–111. doi: 10.3324/haematol.2021.278436
  4. Khoury JD et al. The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Myeloid and Histiocytic/Dendritic Neoplasms. Leukemia. 2022;36:1703–1719. doi: 10.1038/s41375-022-01613-1
  5. Liquori A et al. Acute Promyelocytic Leukemia: A Constellation of Molecular Events around a Single PML-RARA Fusion Gene. Cancers (Basel). 2020;12:624. doi: 10.3390/cancers12030624
  6. Villiers W et al. Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in acute promyelocytic leukemia. Nat Commun. 2023;14:724. doi: 10.1038/s41467-023-36262-0
  7. Sanz MA et al. Management of acute promyelocytic leukemia: updated recommendations from an expert panel of the European LeukemiaNet. Blood. 2019;133:1630–1643. doi: 10.1182/blood-2019-01-894980
  8. Cicconi L et al. Characteristics and outcome of acute myeloid leukemia with uncommon retinoic acid receptor-alpha (RARA) fusion variants. Blood Cancer J. 2021;11:167. doi: 10.1038/s41408-021-00561-w
  9. Matsukawa T and Aplan PD. Clinical and molecular consequences of fusion genes in myeloid malignancies. Stem Cells. 2020;38:1366–1374. doi: 10.1002/stem.3263
  10. van Dongen J et al. Standardized RT-PCR analysis of fusion gene transcripts from chromosome aberrations in acute leukemia for detection of minimal residual disease. Leukemia. 1999;13:1901–1928. doi: 10.1038/sj.leu.2401592.


*RUO, Research Use Only

SureSeq: For Research Use Only; Not for Diagnostic Procedures.

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