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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 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 TP53 -Mutant Myelodysplastic Syndromes (2021) · cites this paper as [3]
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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
Shiozawa, Y., Malcovati, L., Gallì, A., Pellagatti, A., Karimi, M., Sato‐Otsubo, A., Sato, Y., Suzuki, H., Yoshizato, T., Yoshida, K., et al. (2017) · Blood · doi:10.1182/blood-2017-05-783050 · Cited by 82
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 76
Grossmann, V., Bacher, U., Haferlach, C., Schnittger, S., Poetzinger, F., Weißmann, S., Roller, A., Eder, C., Fasan, A., Zenger, M., et al. (2013) · Leukemia · doi:10.1038/leu.2013.144 · Cited by 73
Current and emerging strategies for management of myelodysplastic syndromes
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Consequences of mutant TET2 on clonality and subclonal hierarchy
Hirsch, C. M., Nazha, A., Kneen, K. E., Abazeed, M. E., Meggendorfer, M., Przychodzen, B. P., Nadarajah, N., Ademà, V., Nagata, Y., Goyal, A., et al. (2018) · Leukemia · doi:10.1038/s41375-018-0150-9 · Cited by 71
“Previously, usage of T cells as germ line [13, 29] resulted in similar frequencies of TET2 compared to skin or buccal swabs [27, 30].”
Singhal, D., Wee, L. Y. A., Kutyna, M. M., Chhetri, R., Geoghegan, J., Schreiber, A. W., Feng, J., Wang, P. P.-S., Babic, M., Parker, W. T., et al. (2019) · Leukemia · doi:10.1038/s41375-019-0479-8 · Cited by 62
Invariant phenotype and molecular association of biallelic TET2 mutant myeloid neoplasia
Awada, H. K., Nagata, Y., Goyal, A., Asad, M., Patel, B. J., Hirsch, C. M., Kuzmanovic, T., Guan, Y., Przychodzen, B. P., Aly, M. M., et al. (2019) · Blood Advances · doi:10.1182/bloodadvances.2018024216 · Cited by 68
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Recent advances in understanding clonal haematopoiesis in aplastic anaemia
Stanley, N. L., Olson, T. S., & Babushok, D. V. (2017) · British Journal of Haematology · doi:10.1111/bjh.14510 · Cited by 65
“& 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 65
Self-citationPreleukemia: one name, many meanings
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Genetic characterization of acquired aplastic anemia by targeted sequencing
Heuser, M., Schlarmann, C., Dobbernack, V., Panagiota, V., Wiehlmann, L., Walter, C., Beier, F., Ziegler, P., Yun, H., Kade, S., et al. (2014) · Haematologica · doi:10.3324/haematol.2013.101642 · Cited by 61
Spinella, J.-F., Cassart, P., Richer, C., Saillour, V., Ouimet, M., Langlois, S., St-Onge, P., Sontag, T., Healy, J., Minden, M. D., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.11796 · Cited by 60
Poiré, X., Labopin, M., Maertens, J. A., Yakoub‐Agha, I., Blaise, D., Ifrah, N., Socié, G., Gedde-Dhal, T., Schaap, N. P., Cornelissen, J. J., et al. (2017) · Journal of Hematology & Oncology · doi:10.1186/s13045-017-0393-3 · Cited by 62
Novel recurrent mutations in the RAS-like GTP-binding gene RIT1 in myeloid malignancies
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Duncavage, E. J., & Tandon, B. (2015) · International Journal of Laboratory Hematology · doi:10.1111/ijlh.12361 · Cited by 58
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 58
‘CHIP’ping away at clonal hematopoiesis
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Self-citationFlotho, C., Sommer, S., & Lübbert, M. (2017) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2017.10.011 · Cited by 57
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].”
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“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
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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
Leeke, B. J., Marsman, J., O'Sullivan, J. M., & Horsfield, J. A. (2014) · Experimental Hematology and Oncology · doi:10.1186/2162-3619-3-13 · Cited by 50
“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
Bejar, R. L. (2016) · Current Opinion in Hematology · doi:10.1097/moh.0000000000000313 · Cited by 53
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
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Metadata
- 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
- 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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