| 1. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)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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| 4. |
- Topchiev, N. P., et al.
(author)
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GAMMA-400 gamma-ray observatory
- 2015
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In: Proceedings of Science. - : Proceedings of Science (PoS).
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Conference paper (peer-reviewed)abstract
- The GAMMA-400 gamma-ray telescope with excellent angular and energy resolutions is designed to search for signatures of dark matter in the fluxes of gamma-ray emission and electrons+ positrons.Precision investigations of gamma-ray emission fromGalactic Center, Crab, Vela, Cygnus, Geminga, and other regions will be performed, as well asdiffuse gamma-rayemission,along with measurements of high-energy electron + positron and nuclei fluxes. Furthermore, it will studygamma-ray bursts and gamma-ray emission from the Sun during periods of solar activity. The energy range of GAMMA-400 is expected to be from ∼20 MeV up to TeV energies for gamma rays, up to 10 TeV for electrons + positrons, and up to 1015eV for cosmic-ray nuclei. For high-energy gamma rays with energy from 10 to 100 GeV, the GAMMA-400 angular resolution improves from 0.1° to ∼0.01° and energy resolution from 3% to ∼1%; the proton rejection factor is ∼5x105. GAMMA-400 will be installed onboardthe Russian space observatory.
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| 5. |
- Adriani, O., et al.
(author)
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The gamma-400 space observatory : Status and perspectives
- 2014
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In: Proceedings of Science. - : Sissa Medialab Srl.
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Conference paper (peer-reviewed)abstract
- The present design of the new space observatory GAMMA-400 is presented in this paper. The instrument has been designed for the optimal detection of gamma rays in a broad energy range (from ∼100 MeV up to 3 TeV), with excellent angular and energy resolution. The observatory will also allow precise and high statistic studies of the electron component in the cosmic rays up to the multi TeV region, as well as protons and nuclei spectra up to the knee region. The GAMMA-400 observatory will allow to address a broad range of science topics, like search for signatures of dark matter, studies of Galactic and extragalactic gamma-ray sources, Galactic and extragalactic diffuse emission, gamma-ray bursts and charged cosmic rays acceleration and diffusion mechanism up to the knee.
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| 8. |
- Leonov, A. A., et al.
(author)
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The GAMMA-400 gamma-ray telescope characteristics. Angular resolution and electrons/protons separation
- 2014
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In: Proceedings of Science. - : Sissa Medialab Srl.
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Conference paper (peer-reviewed)abstract
- The measurements of gamma-ray fluxes and cosmic-ray electrons and positrons in the energy range from 100 MeV to several TeV, which will be realized by the specially designed GAMMA-400 gamma-ray telescope, concern with the following broad range of scientific topics. Search for signatures of dark matter, surveying the celestial sphere in order to study point and extended sources of gamma-rays, measuring the energy spectra of Galactic and extragalactic diffuse gamma-ray emission, study of gamma-ray bursts and gamma-ray emission from the Sun, as well as high precision measurements of spectra of high-energy electrons and positrons, protons and nuclei up to the knee. To clarify these scientific problems with the new experimental data the GAMMA-400 gamma-ray telescope possesses unique physical characteristics comparing with previous and present experiments. For gamma-ray energies more than 100 GeV GAMMA-400 provides the energy resolution ~1% and angular resolution better than 0.02 deg. The methods, developed to reconstruct the direction of incident gamma photon, are presented in this paper, as well as, the capability of the GAMMA-400 gamma-ray telescope to distinguish electrons and positrons from protons in cosmic rays is investigated. The first point concerns with the space topology of high-energy gamma photon interaction in the matter of GAMMA-400. Multiple secondary particles, generated inside gamma-ray telescope, produce significant problems to restore the direction of initial gamma photon. Also back-splash particles, i.e., charged particles and gamma photons generated in calorimeter and moved upward, mask the initial tracks of electron/positron pair from conversion of incident gamma photon. The processed methods allow us to reconstruct the direction of electromagnetic shower axis and extract the electron/positron trace. As a result, the direction of incident gamma photon with the energy of 100 GeV is calculated with an accuracy of better than 0.02 deg. The main components of cosmic rays are protons and helium nuclei, whereas the part of lepton component in the total flux is ~10 -3 for high energies. The separate contribution in proton rejection is studied for each detector system of the GAMMA-400 gamma-ray telescope. Using combined information from all detector systems allow us to provide the rejection from protons with a factor of ~4 10 5 for vertical incident particles and ~3 10 5 for particle with initial inclination of 30 deg. Science with the New Generation of High Energy Gamma-ray experiments, 10th Workshop (Scineghe2014) 04-06 June 2014 Lisbon - Portugal.
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| 9. |
- Topchiev, N. P., et al.
(author)
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The GAMMA-400 experiment : Status and prospects
- 2015
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In: Bulletin of the Russian Academy of Sciences: Physics. - 1062-8738. ; 79:3, s. 417-420
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Journal article (peer-reviewed)abstract
- The development of the GAMMA-400 γ-ray telescope continues. The GAMMA-400 is designed to measure fluxes of γ-rays and the electron-positron cosmic-ray component possibly associated with annihilation or decay of dark matter particles; and to search for and study in detail discrete γ-ray sources, to measure the energy spectra of Galactic and extragalactic diffuse γ-rays, and to study γ-ray bursts and γ-rays from the active Sun. The energy range for measuring γ-rays and electrons (positrons) is from 100 MeV to 3000 GeV. For 100-GeV γ-rays, the γ-ray telescope has an angular resolution of ∼0.01°, an energy resolution of ∼1%, and a proton rejection factor of ∼5 × 105. The GAMMA-400 will be installed onboard the Russian Space Observatory.
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| 10. |
- Bar, N., et al.
(author)
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A reference map of potential determinants for the human serum metabolome
- 2020
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In: Nature. - : Nature Research. - 0028-0836 .- 1476-4687. ; 588:7836, s. 135-140
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Journal article (peer-reviewed)abstract
- The serum metabolome contains a plethora of biomarkers and causative agents of various diseases, some of which are endogenously produced and some that have been taken up from the environment1. The origins of specific compounds are known, including metabolites that are highly heritable2,3, or those that are influenced by the gut microbiome4, by lifestyle choices such as smoking5, or by diet6. However, the key determinants of most metabolites are still poorly understood. Here we measured the levels of 1,251 metabolites in serum samples from a unique and deeply phenotyped healthy human cohort of 491 individuals. We applied machine-learning algorithms to predict metabolite levels in held-out individuals on the basis of host genetics, gut microbiome, clinical parameters, diet, lifestyle and anthropometric measurements, and obtained statistically significant predictions for more than 76% of the profiled metabolites. Diet and microbiome had the strongest predictive power, and each explained hundreds of metabolites—in some cases, explaining more than 50% of the observed variance. We further validated microbiome-related predictions by showing a high replication rate in two geographically independent cohorts7,8 that were not available to us when we trained the algorithms. We used feature attribution analysis9 to reveal specific dietary and bacterial interactions. We further demonstrate that some of these interactions might be causal, as some metabolites that we predicted to be positively associated with bread were found to increase after a randomized clinical trial of bread intervention. Overall, our results reveal potential determinants of more than 800 metabolites, paving the way towards a mechanistic understanding of alterations in metabolites under different conditions and to designing interventions for manipulating the levels of circulating metabolites.
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