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UnknownReconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.
The type and genomic context of cancer mutations depend on their causes. These causes have been characterized using signatures that represent mutation types that co-occur in the same tumours. However, it remains unclear how mutation processes change during cancer evolution due to the lack of reliabl...
S-EPMC7002414 | biostudies-literature
UnknownThe landscape of viral associations in human cancers.
Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and-for a subset-whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that ...
S-EPMC8076016 | biostudies-literature
UnknownComprehensive molecular characterization of mitochondrial genomes in human cancers.
Mitochondria are essential cellular organelles that play critical roles in cancer. Here, as part of the International Cancer Genome Consortium/The Cancer Genome Atlas Pan-Cancer Analysis of Whole Genomes Consortium, which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor typ...
S-EPMC7058535 | biostudies-literature
UnknownDivergent mutational processes distinguish hypoxic and normoxic tumours.
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and...
S-EPMC7002770 | biostudies-literature
UnknownPan-cancer analysis of whole genomes.
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour...
S-EPMC7025898 | biostudies-literature
UnknownCombined burden and functional impact tests for cancer driver discovery using DriverPower.
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a sof...
S-EPMC7002750 | biostudies-literature
UnknownCancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.
Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Her...
S-EPMC7002399 | biostudies-literature
UnknownPathway and network analysis of more than 2500 whole cancer genomes.
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as par...
S-EPMC7002574 | biostudies-literature
UnknownIntegrative pathway enrichment analysis of multivariate omics data.
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple...
S-EPMC7002665 | biostudies-literature
UnknownHigh-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report ...
S-EPMC7002524 | biostudies-literature
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