Traditionally, acute myeloid leukemia (AML) diagnosis has relied on morphology and cytogenetic analysis, with a focus on identifying key chromosomal aberrations and translocations. Recurrent cytogenetic abnormalities, such as loss of chromosomes (−5/5q, −7/7q), gain of chromosome (+8), and deletion of 17p, provide critical diagnostic, prognostic, and treatment insights. Techniques like fluorescence in situ hybridization (FISH) help identify these cytogenetic alterations, especially when standard metaphase cytogenetics are insufficient.¹

However, molecular profiling through next-generation sequencing (NGS) has become an essential tool in AML diagnosis, allowing the detection of key mutations and guiding targeted therapies. Molecular testing helps clinicians identify actionable mutations, such as IDH1, IDH2, and FLT3, which are linked to specific therapies. Moreover, RNA sequencing is increasingly used to uncover cryptic gene fusions that may be missed by cytogenetics, thus providing a more comprehensive genetic landscape of AML.¹

Multiple testing methods are used to detect somatic mutations in AML. These include¹:

Each method offers varying degrees of sensitivity and specificity in identifying mutations that inform AML classification, prognosis, and risk stratification. Specific genes like NPM1, FLT3, and CEBPA are crucial in subtyping AML and offering valuable prognostic insights, especially in cases with a normal karyotype (NK).¹ The 2022 European LeukemiaNet (ELN) classification incorporates mutations in genes such as BCOR, EZH2, SF3B1, and TP53 to assign patients to adverse prognostic groups, influencing treatment choices and overall management.²

Recent updates to AML classification systems, such as those by the World Health Organization (WHO) and the International Consensus Classification (ICC), increasingly define AML subtypes based on specific genetic mutations (Figure 1).^3,4 The National Comprehensive Cancer Network (NCCN) guidelines also emphasize the critical importance of molecular profiling in AML management.⁵ These guidelines recommend comprehensive genetic testing for all AML cases as a standard part of the diagnostic workup. These include

• Epigenetic Modifiers: Genes like DNMT3A, TET2, and ASXL1 are frequently mutated in AML, playing a critical role in cellular processes like DNA methylation and chromatin regulation. Mutations in these genes are often early events in AML development and are associated with clonal hematopoiesis of indeterminate potential (CHIP), particularly in older adults.
• Signaling Pathway Mutations: Mutations in signaling genes like FLT3 and the Ras pathway (NRAS, KRAS) disrupt normal hematopoietic growth and differentiation, contributing to AML development. FLT3 mutations, in particular, are targeted by specific inhibitors that are crucial in treatment plans.
• Transcription Factors: Mutations in transcription factors such as RUNX1 and CEBPA occur in about 10% of AML cases. These mutations significantly impact prognosis and are associated with AML subtypes like core-binding factor AML, which generally responds well to treatment.

Cohesin Mutations: Mutations in the cohesin complex genes (SMC1A, SMC3, STAG2) are found in 10%–20% of AML patients and influence chromatin structure and gene expression. These mutations are often associated with poor outcomes and typically cooperate with other mutations like NPM1 and RUNX1.

Molecular testing is invaluable for determining prognosis, guiding treatment decisions, and monitoring for measurable residual disease (MRD) in AML. Mutations in genes like NPM1 are particularly useful for MRD monitoring due to their specificity and stability, offering a reliable predictor of relapse. Conversely, mutations like DNMT3A detected after treatment may indicate the persistence of pre-leukemic clones, rather than active leukemia, and are less useful for MRD monitoring.¹

The integration of molecular testing into AML diagnosis and management has transformed how the disease is classified, treated, and monitored. By identifying key mutations and understanding their clinical implications, healthcare providers can better stratify risk, tailor treatment plans, and improve patient outcomes in AML. As molecular technologies continue to advance, they will play an increasingly central role in guiding therapeutic decisions and enhancing the precision of AML care.

References

1. Wachter F, Pikman Y. Pathophysiology of acute myeloid leukemia. Acta Haematol. 2024;147(2):229-246. doi:10.1159/000536152
2. Döhner H, Wei AH, Appelbaum FR, et al. Diagnosis and management of AML in adults: 2022 recommendations from an international expert panel on behalf of the ELN. Blood. 2022;140(12):1345-1377. doi:10.1182/blood.2022016867
3. Arber DA, Orazi A, Hasserjian RP, et al. International Consensus Classification of Myeloid Neoplasms and Acute Leukemias: integrating morphologic, clinical, and genomic data. Blood. 2022;140(11):1200-1228. doi:10.1182/blood.2022015850
4. Khoury JD, Solary E, Abla O, et al. The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Myeloid and Histiocytic/Dendritic Neoplasms. Leukemia. 2022;36(7):1703-1719. doi:10.1038/s41375-022-01613-1
5. National Comprehensive Cancer Network (NCCN). Acute myeloid leukemia (Version 3.2024). Updated May 17, 2024. Accessed September 30, 2024. https://www.nccn.org/professionals/physician_gls/pdf/aml.pdf
6. What’s new in AML classification (WHO 2022 vs International Consensus Classification). College of American Pathologists. Accessed October 1, 2024. https://www.cap.org/member-resources/articles/whats-new-in-aml-classification-who-2022-vs-international-consensus-classification