| 1. |
- 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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| 2. |
- Hinkley, Sasha, et al.
(författare)
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The JWST Early Release Science Program for the Direct Imaging and Spectroscopy of Exoplanetary Systems
- 2022
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Ingår i: Publications of the Astronomical Society of the Pacific. - : IOP Publishing. - 0004-6280 .- 1538-3873. ; 134:1039
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Tidskriftsartikel (refereegranskat)abstract
- The direct characterization of exoplanetary systems with high-contrast imaging is among the highest priorities for the broader exoplanet community. As large space missions will be necessary for detecting and characterizing exo-Earth twins, developing the techniques and technology for direct imaging of exoplanets is a driving focus for the community. For the first time, JWST will directly observe extrasolar planets at mid-infrared wavelengths beyond 5 μm, deliver detailed spectroscopy revealing much more precise chemical abundances and atmospheric conditions, and provide sensitivity to analogs of our solar system ice-giant planets at wide orbital separations, an entirely new class of exoplanet. However, in order to maximize the scientific output over the lifetime of the mission, an exquisite understanding of the instrumental performance of JWST is needed as early in the mission as possible. In this paper, we describe our 55 hr Early Release Science Program that will utilize all four JWST instruments to extend the characterization of planetary-mass companions to ∼15 μm as well as image a circumstellar disk in the mid-infrared with unprecedented sensitivity. Our program will also assess the performance of the observatory in the key modes expected to be commonly used for exoplanet direct imaging and spectroscopy, optimize data calibration and processing, and generate representative data sets that will enable a broad user base to effectively plan for general observing programs in future Cycles.
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| 3. |
- Zakhozhay, Olga, et al.
(författare)
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Radial Velocity Survey for Planets around Young stars (RVSPY) Target characterisation and high-cadence survey
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 667
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Tidskriftsartikel (refereegranskat)abstract
- Context. The occurrence rate and period distribution of (giant) planets around young stars is still not as well constrained as for older main-sequence stars. This is mostly due to the intrinsic activity-related complications and the avoidance of young stars in many large planet search programmes. Yet, dynamical restructuring processes in planetary systems may last significantly longer than the actual planet formation phase and may well extend long into the debris disc phase, such that the planet populations around young stars may differ from those observed around main-sequence stars.Aims. We introduce our Radial Velocity Survey for Planets around Young stars (RVSPY), which is closely related to the NaCo-ISPY direct imaging survey, characterise our target stars, and search for substellar companions at orbital separations smaller than a few au from the host star.Methods. We used the FEROS spectrograph, mounted to the MPG/ESO 2.2 m telescope in Chile, to obtain high signal-to-noise spectra and time series of precise radial velocities (RVs) of 111 stars, most of which are surrounded by debris discs. Our target stars have spectral types between early F and late K, a median age of 400 Myr, and a median distance of 45 pc. During the initial reconnaissance phase of our survey, we determined stellar parameters and used high-cadence observations to characterise the intrinsic stellar activity, searched for hot companions with orbital periods of up to 10 days, and derived the detection thresholds for longer-period companions. In our analysis we, have included archival spectroscopic data, spectral energy distribution, and data for photometric time series from the TESS mission.Results. For all target stars we determined their basic stellar parameters and present the results of the high-cadence RV survey and activity characterisation. We have achieved a median single-measurement RV precision of 6 m s−1 and derived the short-term intrinsic RV scatter of our targets (median 23 m s−1), which is mostly caused by stellar activity and decays with an age from >100 m s−1 at <20 Myr to <20 m s−1 at >500 Myr. We analysed time series periodograms of the high-cadence RV data and the shape of the individual cross-correlation functions. We discovered six previously unknown close companions with orbital periods between 10 and 100 days, three of which are low-mass stars, and three are in the brown dwarf mass regime. We detected no hot companion with an orbital period <10 days down to a median mass limit of ~1 MJup for stars younger than 500 Myr, which is still compatible with the established occurrence rate of such companions around main-sequence stars. We found significant RV periodicities between 1.3 and 4.5 days for 14 stars, which are, however, all caused by rotational modulation due to starspots. We also analysed the data for TESS photometric time series and found significant periodicities for most of the stars. For 11 stars, the photometric periods are also clearly detected in the RV data. We also derived stellar rotation periods ranging from 1 to 10 days for 91 stars, mostly from the TESS data. From the intrinsic activity-related short-term RV jitter, we derived the expected mass-detection thresholds for longer-period companions, and selected 84 targets for the longer-term RV monitoring.
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