| 1. |
- Campbell, PJ, et al.
(författare)
-
Pan-cancer analysis of whole genomes
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
Tidskriftsartikel (refereegranskat)abstract
- 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 types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
|
|
| 2. |
|
|
| 3. |
- Leebens-Mack, James H., et al.
(författare)
-
One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
-
Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
-
Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
|
|
| 4. |
|
|
| 5. |
- Zhang, Xingliang, et al.
(författare)
-
Challenges in defining the base of Cambrian Series 2 and Stage 3
- 2017
-
Ingår i: Earth-Science Reviews. - : Elsevier BV. - 0012-8252. ; 172, s. 124-139
-
Tidskriftsartikel (refereegranskat)abstract
- Formal subdivision of the Cambrian System into four series and ten stages is in progress. The base of Cambrian Stage 3 (provisional), which is conterminous with the base of Cambrian Series 2 (provisional), is expected to be placed at a horizon close to the first appearance of trilobites, which marks the onset of the largest phase of the Cambrian explosion. Conceptually, an ideal boundary position would be marked by a significant and globally recognizable bioevent that divides the lower part of the Cambrian System into a sub-trilobitic Terreneuvian Series and a trilobite-dominated Series 2. If the level is to be identified principally through biostratigraphic means, its position also needs to be recognizable using non-biostratigraphic means, and its correlation potential should be tested through detailed investigation of several continuous successions embracing the critical interval. Major difficulties in identifying a suitable horizon include strong biotic provincialism, a plethora of regional unconformities, and facies changes on different paleocontinents in the Cambrian Terreneuvian–Series 2 boundary interval. Levels that provide potential for intercontinental correlation include the first appearance position of trilobites and the approximately equivalent first appearance positions of certain small shelly fossil and acritarch species. In addition, a non-biostratigraphic marker, such as a stable carbon isotopic excursion, may be useful as a correlation level. Cambrian Series 2 and Stage 3 are provisional stratigraphic units, and their conterminous base was previously suggested to coincide to the appearance of trilobites. Compared to other potential chronostratigraphic indicators, the first appearance of trilobites still has advantages for recognizing and correlating the base of Stage 3, and should remain as the provisional primary marker for the boundary position.
|
|
