Laying the foundation for genomically-based risk assessment in chronic myeloid leukemia
Open accessAbstract
Outcomes for patients with chronic myeloid leukemia (CML) have substantially improved due to advances in drug development and rational treatment intervention strategies. Despite these significant advances there are still unanswered questions on patient management regarding how to more reliably predict treatment failure at the time of diagnosis and how to select frontline tyrosine kinase inhibitor (TKI) therapy for optimal outcome. The BCR-ABL1 transcript level at diagnosis has no established prognostic impact and cannot guide frontline TKI selection. BCR-ABL1 mutations are detected in ~50% of TKI resistant patients but are rarely responsible for primary resistance. Other resistance mechanisms are largely uncharacterized and there are no other routine molecular testing strategies to facilitate the evaluation and further stratification of TKI resistance. Advances in next-generation sequencing technology has aided the management of a growing number of other malignancies, enabling the incorporation of somatic mutation profiles in diagnosis, classification, and prognostication. A largely unexplored area in CML research is whether expanded genomic analysis at diagnosis, resistance, and disease transformation can enhance patient management decisions, as has occurred for other cancers. The aim of this article is to review publications that reported mutated cancer-associated genes in CML patients at various disease phases. We discuss the frequency and type of such variants at initial diagnosis and at the time of treatment failure and transformation. Current limitations in the evaluation of mutants and recommendations for future reporting are outlined. The collective evaluation of mutational studies over more than a decade suggests a limited set of cancer-associated genes are indeed recurrently mutated in CML and some at a relatively high frequency. Genomic studies have the potential to lay the foundation for improved diagnostic risk classification according to clinical and genomic risk, and to enable more precise early identification of TKI resistance.
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Somatic mutations in genes other than BCR::ABL1 are found in approximately 20-30% of patients with CML, more commonly in advanced phase than chronic phase disease.
“Somatic mutations in genes other than BCR::ABL1 are found in approximately 20–30% of patients, more commonly in advanced rather than chronic phase disease [9, 10].”
From 2025 European LeukemiaNet recommendations for the management of chronic myeloid leukemia (2025) · cites this paper as [10]
The ‘Mutational landscape at advanced phase CML’ section reports mutations in cancer-associated genes in 77–79% of patients in two blast-crisis studies, supporting their greater frequency in advanced disease. The ‘Mutational landscape at CML diagnosis’ section cautions that the available studies cannot establish the actual frequency at chronic-phase diagnosis. The paper therefore does not support the claim’s approximately 20–30% figure for patients with CML generally. No page numbers were available in our copy. (LLM, conf=0.85)
Experimental — accuracy not yet measuredASXL1 mutations are found in about 10% of patients with CML and seem more frequent in children and young adults.
“ASXL1 mutations are found in about 10% of patients and interestingly seem more frequent in children and young adults [10].”
From 2025 European LeukemiaNet recommendations for the management of chronic myeloid leukemia (2025) · cites this paper as [10]
No molecular markers currently predict treatment failure at diagnosis or guide selection of first-line TKI therapy for optimal outcomes in CML.
“However, there are no molecular markers that predict treatment failure at the time of diagnosis or for selection of first-line TKI therapy for optimal outcomes (22).”
From Discovery of a Novel CIP2A Variant (NOCIVA) with Clinical Relevance in Predicting TKI Resistance in Myeloid Leukemias (2021) · cites this paper as [22]
An expert group recently emphasized the urgent clinical utility of an assay for selecting first-line TKI therapy in CML.
“The urgent clinical utility of such an assay for CML patient first-line TKI therapy selection was recently highlighted by an expert group (22).”
From Discovery of a Novel CIP2A Variant (NOCIVA) with Clinical Relevance in Predicting TKI Resistance in Myeloid Leukemias (2021) · cites this paper as [22]
No patient stratification markers currently guide first-line TKI selection for optimal CML outcomes.
“However, currently, there are no patient stratification markers to guide clinicians in the selection of first-line TKI therapy to achieve optimal outcomes in patients with CML (22).”
From Discovery of a Novel CIP2A Variant (NOCIVA) with Clinical Relevance in Predicting TKI Resistance in Myeloid Leukemias (2021) · cites this paper as [22]
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Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers
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Molecular Profiling of Blastic Transformation in Chronic Myeloid Leukemia
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2025 European LeukemiaNet recommendations for the management of chronic myeloid leukemia
Apperley, J. F., Milojkovic, D., Cross, N. C. P., Hjorth-Hansen, H., Hochhaus, A., Kantarjian, H., Lipton, J. H., Malhotra, H., Niederwieser, D., Radich, J., et al. (2025) · Leukemia · doi:10.1038/s41375-025-02664-w · Cited by 139 · see citing works
“Somatic mutations in genes other than BCR::ABL1 are found in approximately 20 – 30% of patients, more commonly in advanced rather than chronic phase disease [9, 10].”
Self-citationCross, N. C. P., Ernst, T., Branford, S., Cayuela, J.-M., Deininger, M., Fabarius, A., Kim, D. D. H., Machova Polakova, K., Radich, J. P., Hehlmann, R., et al. (2023) · Leukemia · doi:10.1038/s41375-023-02048-y · Cited by 120 · see citing works
Self-citationMutation accumulation in cancer genes relates to nonoptimal outcome in chronic myeloid leukemia
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Self-citationPrognostic impact of ASXL1 mutations in chronic phase chronic myeloid leukemia
Bidikian, A., Kantarjian, H., Jabbour, E., Short, N. J., Patel, K., Ravandi, F., Sasaki, K., & Issa, G. C. (2022) · Blood Cancer Journal · doi:10.1038/s41408-022-00742-1 · Cited by 55 · see citing works
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- Authors
- on behalf of the International CML Foundation Genomics Alliance, Branford, S., Kim, D. D. H., Apperley, J. F., Eide, C. A., Mustjoki, S., Ong, S. T., Nteliopoulos, G., Ernst, T., Chuah, C., Gambacorti-Passerini, C., Mauro, M. J., Druker, B. J., Kim, D.-W., Mahon, F.-X., Cortes, J., Radich, J. P., Hochhaus, A., & Hughes, T. P.
- Affiliations
- South Australia Pathology (AU)
- University Health Network (CA)
- Hammersmith Hospital (GB)
- Howard Hughes Medical Institute (US)
- University of Helsinki (FI)
- Singapore General Hospital (SG)
- Jena University Hospital (DE)
- Azienda Ospedaliera San Gerardo (IT)
- Memorial Sloan Kettering Cancer Center (US)
- Fred Hutch Cancer Center (US)
- Corresponding author
- Branford, Susan
- ORCID
- Venue
- Leukemia
- Published
- 2019-06-17
- Volume
- 33
- Issue
- 8
- Pages
- 1835-1850
- ISSN
- 0887-6924 (ISSN-L)
- 1476-5551
- PMC
- PMC6893870
- OpenAlex
- W2950655888
- Cited by
- 149
- References
- 104
- Citations by year
- 2026: 13 · 2025: 11 · 2024: 15 · 2023: 28 · 2022: 28 · 2021: 23 · 2020: 21 · 2019: 10
- FWCI
- 3.27
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Leukemia (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- BOA (University of Milano-Bicocca) (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Spiral (Imperial College London) (submittedVersion)
- UniSA Research Outputs Repository (University of South Australia) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institute for Health and Care Research (NF-SI-0617-10126, NF-SI-0611-10275)
- National Cancer Institute (R01CA065823, P30CA008748)
- Topics
- Health Sciences › Medicine › Hematology › Chronic Myeloid Leukemia Treatments
- Health Sciences › Medicine › Genetics › Chronic Lymphocytic Leukemia Research
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Lung Cancer Treatments and Mutations
- Keywords
- chronic myeloid leukemia, tyrosine kinase inhibitors, tyrosine kinase inhibitor resistance, BCR-ABL mutations, somatic mutations, cancer genes, disease transformation, prognostic factors, next-generation sequencing
- MeSH terms
- Hematopoiesis, Humans, Mutation, Protein-Tyrosine Kinases, Repressor Proteins, Leukemia, Myelogenous, Chronic, BCR-ABL Positive, Risk Assessment, Protein Kinase Inhibitors, Genes, Neoplasm
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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