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Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
Open accessAbstract
BACKGROUND: Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet clear. METHODS: We analyzed the genomes of 200 clinically annotated adult cases of de novo AML, using either whole-genome sequencing (50 cases) or whole-exome sequencing (150 cases), along with RNA and microRNA sequencing and DNA-methylation analysis. RESULTS: AML genomes have fewer mutations than most other adult cancers, with an average of only 13 mutations found in genes. Of these, an average of 5 are in genes that are recurrently mutated in AML. A total of 23 genes were significantly mutated, and another 237 were mutated in two or more samples. Nearly all samples had at least 1 nonsynonymous mutation in one of nine categories of genes that are almost certainly relevant for pathogenesis, including transcription-factor fusions (18% of cases), the gene encoding nucleophosmin (NPM1) (27%), tumor-suppressor genes (16%), DNA-methylation-related genes (44%), signaling genes (59%), chromatin-modifying genes (30%), myeloid transcription-factor genes (22%), cohesin-complex genes (13%), and spliceosome-complex genes (14%). Patterns of cooperation and mutual exclusivity suggested strong biologic relationships among several of the genes and categories. CONCLUSIONS: We identified at least one potential driver mutation in nearly all AML samples and found that a complex interplay of genetic events contributes to AML pathogenesis in individual patients. The databases from this study are widely available to serve as a foundation for further investigations of AML pathogenesis, classification, and risk stratification. (Funded by the National Institutes of Health.).
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“in line with clinical observations of adults and patients with myeloid malignancies typically lacking this oncogene (43).”
From PU.1-Dependent Enhancer Inhibition Separates Tet2 -Deficient Hematopoiesis from Malignant Transformation (2022) · cites this paper as [43]
Experimental — accuracy not yet measuredIn the citing paper
“both TET2 and TET3 are highly expressed in our model and in human AML27 (Supplementary Figure S2d).”
From Vitamin C-induced epigenomic remodelling in IDH1 mutant acute myeloid leukaemia (2018) · cites this paper as [27]
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“But many of the most commonly seen mutations in CHIP are also recurrent drivers of AML 64, myelodysplastic syndrome (MDS) 65–67, myeloproliferative neoplasms 68, and certain lymphomas 69,70.”
From Clonal hematopoiesis in human aging and disease (2019) · cites this paper as [64]
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“Treatment of AML with targeted therapies is particularly promising due to the fact that AMLs have far fewer mutations than most other adult cancers, with an average of only 13 mutations (Mardis et al, 2009; Cancer Genome Atlas Research Network, 2013).”
From Unlocking the potential of retinoic acid in anticancer therapy (2014) · cites this paper as Cancer Genome Atlas Research Network, 2013
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Metadata
- Authors
- The Cancer Genome Atlas Research Network
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- The Cancer Genome Atlas Research Network
- Venue
- New England Journal of Medicine
- Publisher
- Massachusetts Medical Society
- Published
- 2013-05-30
- Volume
- 368
- Issue
- 22
- Pages
- 2059-2074
- ISSN
- 0028-4793 (ISSN-L)
- 1533-4406
- PMC
- PMC3767041
- OpenAlex
- W1255676896
- Cited by
- 5,078
- References
- 49
- Citations by year
- 2026: 195 · 2025: 277 · 2024: 335 · 2023: 415 · 2022: 465 · 2021: 509 · 2020: 485 · 2019: 466 · 2018: 361 · 2017: 424 · 2016: 382 · 2015: 343 · 2014: 304 · 2013: 108
- FWCI
- 271.87
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- New England Journal of Medicine (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
- eSpace (Curtin University) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U54HG003067, U54HG003079, U54HG003273, R01HG005690)
- National Cancer Institute (R01CA083962, U24CA143882, U24CA143843, U24CA143840, U24CA143858, U24CA144025, U24CA143866, U24CA143883, U24CA143845, R01CA162086, U24CA143867, U24CA143848, U24CA143799, U24CA143835, P01CA101937, P30CA016672, 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 › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- acute myeloid leukemia, de novo AML, adult AML, somatic mutations, epigenetics, DNA methylation, transcription factor fusion, NPM1, tumor suppressor, chromatin modifiers, driver mutations, risk stratification
- MeSH terms
- Nucleophosmin, Adult, Female, Humans, Male, Middle Aged, Mutation, Leukemia, Myeloid, Acute, Gene Expression, Genome, Human, Sequence Analysis, DNA, CpG Islands, DNA Methylation, MicroRNAs, Gene Fusion, Epigenomics
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