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Open AccessAuthor Correction: A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
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Open AccessFocal disruption of DNA methylation dynamics at enhancers in IDH-mutant AML cells
Recurrent mutations in IDH1 or IDH2 in acute myeloid leukemia (AML) are associated with increased DNA methylation, but the genome-wide patterns of this hypermethylation phenotype have not been comprehensively stu...
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Open AccessFunctional and epigenetic phenotypes of humans and mice with DNMT3A Overgrowth Syndrome
Germline pathogenic variants in DNMT3A were recently described in patients with overgrowth, obesity, behavioral, and learning difficulties (DNMT3A Overgrowth Syndrome/DOS). Somatic mutations in the DNMT3A gene ar...
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Open AccessCo-evolution of tumor and immune cells during progression of multiple myeloma
Multiple myeloma (MM) is characterized by the uncontrolled proliferation of plasma cells. Despite recent treatment advances, it is still incurable as disease progression is not fully understood. To investigate...
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Open AccessLong non-coding RNA RAMS11 promotes metastatic colorectal cancer progression
Colorectal cancer (CRC) is the most common gastrointestinal malignancy in the U.S.A. and approximately 50% of patients develop metastatic disease (mCRC). Despite our understanding of long non-coding RNAs (lncR...
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Open AccessA general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
Virtually all tumors are genetically heterogeneous, containing mutationally-defined subclonal cell populations that often have distinct phenotypes. Single-cell RNA-sequencing has revealed that a variety of tum...
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Open AccessDNMT3AR882-associated hypomethylation patterns are maintained in primary AML xenografts, but not in the DNMT3AR882C OCI-AML3 leukemia cell line
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Open AccessCellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential
Hematopoietic clones harboring specific mutations may expand over time. However, it remains unclear how different cellular stressors influence this expansion. Here we characterize clonal hematopoiesis after tw...
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Open AccessVisualizing tumor evolution with the fishplot package for R
Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into t...
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Open AccessPatterns and functional implications of rare germline variants across 12 cancer types
Large-scale cancer sequencing data enable discovery of rare germline cancer susceptibility variants. Here we systematically analyse 4,034 cases from The Cancer Genome Atlas cancer cases representing 12 cancer ...
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Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia
Somatic TP53 mutations are highly prevalent in therapy-related acute myeloid leukaemia and myelodysplastic syndrome, which arise as complications of cytotoxic chemotherapy or radiotherapy; although it was believe...
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Age-related mutations associated with clonal hematopoietic expansion and malignancies
Systematic analysis of cancer-associated mutations in the blood cells of healthy individuals.
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DGIdb: mining the druggable genome
A database of known drug-gene interactions, with information derived from many public sources, allows the identification of genes that are currently targeted by a drug and the membership of genes in a category...
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Open AccessMutational landscape and significance across 12 major cancer types
The Cancer Genome Atlas (TCGA) has used the latest sequencing and analysis methods to identify somatic variants across thousands of tumours. Here we present data and analytical results for point mutations and ...
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Open AccessBreakTrans: uncovering the genomic architecture of gene fusions
Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance...
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Erratum: The Pediatric Cancer Genome Project
Nat. Genet. 44, 619–622 (2012); published online 29 May 2012; corrected after print 9 July 2012 In the version of this article initially published, there were errors in the labeling of Figure 1b. Specifically,...
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The Pediatric Cancer Genome Project
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Open AccessWhole-genome analysis informs breast cancer response to aromatase inhibition
To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, we studied pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant ar...
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Open AccessClonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
The sequencing of AML genomes of eight patients before and after relapse reveals two major patterns of clonal evolution, with chemotherapy appearing to have a role in both patterns.
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Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
Matthew Walter and colleagues report the whole-genome sequencing of a secondary acute myeloid leukemia sample and a matched normal tissue sample. Further analysis of additional subjects identified recurrent mu...
