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Pan-cancer deconvolution of tumour composition using DNA methylation.
(NATURE PUBLISHING GROUP, 2018-08-13)
The nature and extent of immune cell infiltration into solid tumours are key determinants of therapeutic response. Here, using a DNA methylation-based approach to tumour cell fraction deconvolution, we report the integrated ...
Whole-genome sequencing of multiple myeloma reveals oncogenic pathways are targeted somatically through multiple mechanisms.
(2018-11)
Multiple myeloma (MM) is a biologically heterogeneous malignancy, however, the mechanisms underlying this complexity are incompletely understood. We report an analysis of the whole-genome sequencing of 765 MM patients from ...
Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress.
(OXFORD UNIV PRESS, 2014-01-01)
In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage. These canonical activities can be repressed by ...
Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes.
(AMER ASSOC ADVANCEMENT SCIENCE, 2014-08-01)
Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive ...
Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
(NATURE PUBLISHING GROUP, 2016-06-02)
We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding ...
GENCODE reference annotation for the human and mouse genomes.
(OXFORD UNIV PRESS, 2019-01-08)
The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 ...
Genomic alterations in breast cancer: level of evidence for actionability according to ESMO Scale for Clinical Actionability of molecular Targets (ESCAT).
(ELSEVIER, 2019-03-01)
Better knowledge of the tumor genomic landscapes has helped to develop more effective targeted drugs. However, there is no tool to interpret targetability of genomic alterations assessed by next-generation sequencing in ...
Evolutionary dynamics of residual disease in human glioblastoma.
(OXFORD UNIV PRESS, 2019-03-01)
BACKGROUND: Glioblastoma is the most common and aggressive adult brain malignancy against which conventional surgery and chemoradiation provide limited benefit. Even when a good treatment response is obtained, recurrence ...
MDC1 Interacts with TOPBP1 to Maintain Chromosomal Stability during Mitosis.
(CELL PRESS, 2019-05-02)
In mitosis, cells inactivate DNA double-strand break (DSB) repair pathways to preserve genome stability. However, some early signaling events still occur, such as recruitment of the scaffold protein MDC1 to phosphorylated ...
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.
(COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2019-12-01)
The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify ...