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- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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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.
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- Carlevaro-Fita, J, et al.
(författare)
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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
- 2020
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1, s. 56-
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Tidskriftsartikel (refereegranskat)abstract
- 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. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
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- Eckert, EM, et al.
(författare)
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Every fifth published metagenome is not available to science.
- 2020
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1545-7885. ; 18:4
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Tidskriftsartikel (refereegranskat)abstract
- Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high-impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions-a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.
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- Isacson, Maths, Professor em. 1948-, et al.
(författare)
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Arbete & gemenskap : vardagsbilder från Uppsala 1985-1994
- 2020
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Bok (populärvet., debatt m.m.)abstract
- Under 1980-talet och början av 1990-talet gjorde jag ett drygt sjuttiotal uppdrag för tidningen Uppsala-Demokraten. Jag fotograferade med Nikon FE och Nikon F3, två kameror jag trivdes bra med och som var otroligt pålitliga. I kameraväskan fanns dessutom ett flertal objektiv, en stor Metz-blixt, mängder av Tri-X-filmer samt ett flertal batterier. Bara till en kameramotor behövdes åtta sådana. Väskan var tung att bära på, den slet på rygg och axlar. Uppdragen var alltid att skildra människor, såväl på arbetsplatser som i folkparker och på andra offentliga platser. Jag hade stor frihet att fotografera på mitt eget sätt och att närma mig människor efter egen förmåga. Det var sällan några var negativa till att bli fotograferade. När uppdragen skulle publiceras hade jag ett rikt material att utgå ifrån, och idag, nästan fyrtio år senare, ligger det till grund för denna bok.Många av bilderna har aldrig tidigare visats. Ett fotografi är knutet till en bestämd tid och verklighet samtidigt som det är tidlöst och kan ses om och om igen, när som helst. Som betraktare fyller vi bilden med innehåll, känslor och betydelser, såsom jag fyller bilderna i min fotobokssamling. Med hjälp av det skrivna ordet kan man sedan förankra det avfotograferade i tid och miljö och fördjupa dess sammanhang. Det har Maths Isacson, professor emeritus i ekonomisk historia, och Bo Larsson, förutvarande antikvarie på Upplandsmuseet, numera på Stadsmuseet i Stockholm, gjort. Jag tror att deras ord och mina bilder tillsammans kan öka förståelsen för människors liv och vardag i ett Uppsala som visserligen ligger nära i tiden, men som ändå är förgånget.
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