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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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- Abbafati, Cristiana, et al.
(författare)
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- 2020
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Tidskriftsartikel (refereegranskat)
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- Palmese, A., et al.
(författare)
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Stellar mass as a galaxy cluster mass proxy : application to the Dark Energy Survey redMaPPer clusters
- 2020
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Ingår i: \mnras. - : Oxford University Press (OUP). ; 493:4, s. 4591-4606
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Tidskriftsartikel (refereegranskat)abstract
- We introduce a galaxy cluster mass observable, μ⋆, based on the stellar masses of cluster members, and we present results for the Dark Energy Survey (DES) Year 1 (Y1) observations. Stellar masses are computed using a Bayesian model averaging method, and are validated for DES data using simulations and COSMOS data. We show that μ⋆ works as a promising mass proxy by comparing our predictions to X-ray measurements. We measure the X-ray temperature–μ⋆ relation for a total of 129 clusters matched between the wide-field DES Y1 redMaPPer catalogue and Chandra and XMM archival observations, spanning the redshift range 0.1 < z < 0.7. For a scaling relation that is linear in logarithmic space, we find a slope of α = 0.488 ± 0.043 and a scatter in the X-ray temperature at fixed μ⋆ of σlnTX|μ⋆=0.266+0.019−0.020 for the joint sample. By using the halo mass scaling relations of the X-ray temperature from the Weighing the Giants program, we further derive the μ⋆-conditioned scatter in mass, finding σlnM|μ⋆=0.26+0.15−0.10. These results are competitive with well-established cluster mass proxies used for cosmological analyses, showing that μ⋆ can be used as a reliable and physically motivated mass proxy to derive cosmological constraints.
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- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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- Bluhm, P., et al.
(författare)
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Precise mass and radius of a transiting super-Earth planet orbiting the M dwarf TOI-1235: a planet in the radius gap?
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 639
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Tidskriftsartikel (refereegranskat)abstract
- We report the confirmation of a transiting planet around the bright weakly active M0.5 V star TOI-1235 (TYC 4384-1735-1, V ≈ 11.5 mag), whose transit signal was detected in the photometric time series of sectors 14, 20, and 21 of the TESS space mission. We confirm the planetary nature of the transit signal, which has a period of 3.44 d, by using precise RV measurements with the CARMENES, HARPS-N, and iSHELL spectrographs, supplemented by high-resolution imaging and ground-based photometry. A comparison of the properties derived for TOI-1235 b with theoretical models reveals that the planet has a rocky composition, with a bulk density slightly higher than that of Earth. In particular, we measure a mass of Mp = 5.9 ± 0.6 M⊕ and a radius of Rp = 1.69 ± 0.08 R⊕, which together result in a density of ρp = 6.7- 1.1+ 1.3 g cm-3. When compared with other well-characterized exoplanetary systems, the particular combination of planetary radius and mass places our discovery in the radius gap, which is a transition region between rocky planets and planets with significant atmospheric envelopes. A few examples of planets occupying the radius gap are known to date. While the exact location of the radius gap for M dwarfs is still a matter of debate, our results constrain it to be located at around 1.7 R⊕ or larger at the insolation levels received by TOI-1235 b (~60 S⊕). This makes it an extremely interesting object for further studies of planet formation and atmospheric evolution.
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