Clonal diversity of recurrently mutated genes in myelodysplastic syndromes
Open accessAbstract
Recent studies suggest that most cases of myelodysplastic syndrome (MDS) are clonally heterogeneous, with a founding clone and multiple subclones. It is not known whether specific gene mutations typically occur in founding clones or subclones. We screened a panel of 94 candidate genes in a cohort of 157 patients with MDS or secondary acute myeloid leukemia (sAML). This included 150 cases with samples obtained at MDS diagnosis and 15 cases with samples obtained at sAML transformation (8 were also analyzed at the MDS stage). We performed whole-genome sequencing (WGS) to define the clonal architecture in eight sAML genomes and identified the range of variant allele frequencies (VAFs) for founding clone mutations. At least one mutation or cytogenetic abnormality was detected in 83% of the 150 MDS patients and 17 genes were significantly mutated (false discovery rate ≤0.05). Individual genes and patient samples displayed a wide range of VAFs for recurrently mutated genes, indicating that no single gene is exclusively mutated in the founding clone. The VAFs of recurrently mutated genes did not fully recapitulate the clonal architecture defined by WGS, suggesting that comprehensive sequencing may be required to accurately assess the clonal status of recurrently mutated genes in MDS.
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TP53 gene mutations are detected in approximately 10%-20% of patients with de novo MDS or AML and 30%-40% of patients with therapy-related disease.
“TP53 gene mutations are detected in approximately 10%-20% of patients with de novo myelodysplastic syndromes (MDS)1-4 or acute myeloid leukemia (AML)5,6 and 30%-40% of patients with therapy-related disease.7”
From Eprenetapopt (APR-246) and Azacitidine in <i>TP53</i> -Mutant Myelodysplastic Syndromes (2021) · cites this paper as [3]
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“Median (range) 10 (4-45) Cytogenetic risk, No.”
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BackgroundProtein Arginine Methyltransferase 5 (PRMT5) Inhibitors in Oncology Clinical Trials: A review
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BackgroundMethodInfluentialSelf-citationSplicing factor gene mutations in hematologic malignancies
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Mutation Clearance after Transplantation for Myelodysplastic Syndrome
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Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome
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Biological background of the genomic variations of cf-DNA in healthy individuals
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Mutations of myelodysplastic syndromes (MDS): An update
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Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy
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“12, 17, 22, 23 Most tumors have several recognized driver mutations that are variably distributed between the founding clone and subclones, yielding an enormous number of combinations that might be important to tumorigenesis and outcomes.”
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Mutations in G protein β subunits promote transformation and kinase inhibitor resistance
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How we treat higher-risk myelodysplastic syndromes
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Clinical and genetic predictors of prognosis in myelodysplastic syndromes
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CHIP, CCUS, and Other Acronyms: Definition, Implications, and Impact on Practice
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Germline ETV6 mutations and predisposition to hematological malignancies
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Gene expression and risk of leukemic transformation in myelodysplasia
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Cohesin Mutations in CancerPreprint
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“Increased chromatin accessibility was observed in regions enriched for DNA-binding motifs of ERG, GATA2, and RUNX1, all transcription factors (TFs) involved in maintenance of the stem-cell program in HSPCs (Wilson et al. 2010).”
BackgroundThe genetic and molecular pathogenesis of myelodysplastic syndromes
Shallis, R. M., Ahmad, R., & Zeidan, A. M. (2018) · European Journal Of Haematology · doi:10.1111/ejh.13092 · Cited by 74 · see citing works
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Current and emerging strategies for management of myelodysplastic syndromes
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Consequences of mutant TET2 on clonality and subclonal hierarchy
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“Previously, usage of T cells as germ line [13, 29] resulted in similar frequencies of TET2 compared to skin or buccal swabs [27, 30].”
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Invariant phenotype and molecular association of biallelic TET2 mutant myeloid neoplasia
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Recent advances in understanding clonal haematopoiesis in aplastic anaemia
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“& Graubert, T.A. (2013) Clonal diversity of recurrently mutated genes in myelodysplastic syndromes.”
BackgroundSubclones dominate at MDS progression following allogeneic hematopoietic cell transplant
Jacoby, M. A., Duncavage, E. J., Chang, G. S., Miller, C. A., Shao, J., Elliott, K., Robinson, J., Fulton, R. S., Fronick, C. C., O’Laughlin, M. D., et al. (2018) · JCI Insight · doi:10.1172/jci.insight.98962 · Cited by 64 · see citing works
Self-citationPreleukemia: one name, many meanings
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Genetic characterization of acquired aplastic anemia by targeted sequencing
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Novel recurrent mutations in the RAS-like GTP-binding gene RIT1 in myeloid malignancies
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Pellagatti, A., Roy, S., Genua, C. D., Burns, A., McGraw, K. L., Valletta, S., Larráyoz, M. J., Fernández‐Mercado, M., Mason, J., Killick, S. B., et al. (2015) · Leukemia · doi:10.1038/leu.2015.129 · Cited by 57 · see citing works
‘CHIP’ping away at clonal hematopoiesis
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Anemia as the Main Manifestation of Myelodysplastic Syndromes
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Clinical Significance of DNA Variants in Chronic Myeloid Neoplasms
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MDS prognostic scoring systems – Past, present, and future
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“Genes have been sequenced in several large series of MDS patients using targeted gene set approaches [63e65] or whole exome or genome sequencing [66].”
ResultTamari, R., Chung, S. S., Papadopoulos, E. B., Jakubowski, A. A., Hilden, P. D., Devlin, S. M., Goldberg, J. D., Perales, M., Ponce, D. M., Sauter, C. S., et al. (2015) · Transplantation and Cellular Therapy · doi:10.1016/j.bbmt.2015.07.010 · Cited by 53 · see citing works
“INTRODUCTION Over the past few years, there have been major advances in understanding the biology of myelodysplastic syndrome (MDS), particularly regarding the role of molecular mutations in predicting outcomes [1-6].”
BackgroundCleven, A. H. G., Nardi, V., Ok, C. Y., Goswami, M., Cin, P. D., Zheng, Z., Iafrate, A. J., Hamid, M. A. A., Wang, S. A., & Hasserjian, R. P. (2014) · Modern Pathology · doi:10.1038/modpathol.2014.153 · Cited by 50 · see citing works
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Inferring mutational timing and reconstructing tumour evolutionary histories
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“005 their findings in an extension cohort of secondary AML cases [79].”
BackgroundCohesin mutations in myeloid malignancies: underlying mechanisms
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“Our calculation of the rate of cohesin mutations in AML using the TCGA data [20,21] and other published studies to date [22-28] indicates that the total rate of cohesin mutation in AML is around 9% (Figure 1, Table 1).”
MethodImplications of molecular genetic diversity in myelodysplastic syndromes
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Monosomy 7 in Pediatric Myelodysplastic Syndromes
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The clonal origins of leukemic progression of myelodysplasia
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The biology and clinical impact of genetic lesions in myeloid malignancies
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Splice factor mutations and alternative splicing as drivers of hematopoietic malignancy
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“U2AF1 mutations are associated with ASXL1 (88, 109), RUNX1 (62), and DNMT3A (88, 109) mutations.”
BackgroundInfluentialLarge-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers
Feusier, J. E., Arunachalam, S., Tashi, T., Baker, M. J., Vansant-Webb, C. H., Ferdig, A., Welm, B. E., Rodríguez-Flores, J. L., Ours, C., Jorde, L. B., et al. (2021) · Blood Cancer Discovery · doi:10.1158/2643-3230.bcd-20-0094 · Cited by 42 · see citing works
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- Authors
- Walter, M. J., Shen, D., Shao, J., Ding, L., White, B. S., Kandoth, C., Miller, C. A., Niu, B., McLellan, M. D., Dees, N. D., Fulton, R., Elliot, K., Heath, S., Grillot, M., Westervelt, P., Link, D. C., DiPersio, J. F., Mardis, E., Ley, T. J., Wilson, R. K., & Graubert, T. A.
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- Graubert, T A
- ORCID
- Venue
- Leukemia
- Published
- 2013-02-27
- Volume
- 27
- Issue
- 6
- Pages
- 1275-1282
- ISSN
- 0887-6924 (ISSN-L)
- 1476-5551
- PMC
- PMC3736571
- OpenAlex
- W2041596445
- Cited by
- 284
- References
- 31
- Citations by year
- 2026: 1 · 2025: 8 · 2024: 7 · 2023: 9 · 2022: 20 · 2021: 15 · 2020: 16 · 2019: 15 · 2018: 29 · 2017: 36 · 2016: 32 · 2015: 34 · 2014: 37 · 2013: 23 · 2012: 2
- FWCI
- 30.13
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Leukemia (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Heart, Lung, and Blood Institute (RC2HL102927, R01HL082973)
- National Human Genome Research Institute (U01HG006517, U54HG003079)
- National Cancer Institute (P01CA101937, P30CA091842)
- Topics
- Health Sciences › Medicine › Hematology › Acute Myeloid Leukemia Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- myelodysplastic syndrome, clonal heterogeneity, subclones, variant allele frequency, secondary acute myeloid leukemia, clonal architecture, chromosomal abnormalities
- MeSH terms
- Female, Gene Frequency, Humans, Male, Middle Aged, Mutation, Myelodysplastic Syndromes, Recurrence, Leukemia, Myeloid, Acute
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