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| 2. |
- 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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| 3. |
- Rheinbay, E, et al.
(författare)
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 102-
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
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| 4. |
- 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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| 5. |
- Diakaki, M., et al.
(författare)
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Towards the high-accuracy determination of the 238U fission cross section at the threshold region at CERN -€“ n_TOF
- 2016
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Ingår i: EPJ Web of Conferences. - : EDP Sciences. - 2100-014X.
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Konferensbidrag (refereegranskat)abstract
- The U-238 fission cross section is an international standard beyond 2 MeV where the fission plateau starts. However, due to its importance in fission reactors, this cross-section should be very accurately known also in the threshold region below 2 MeV. The U-238 fission cross section has been measured relative to the U-235 fission cross section at CERN - n_TOF with different detection systems. These datasets have been collected and suitably combined to increase the counting statistics in the threshold region from about 300 keV up to 3 MeV. The results are compared with other experimental data, evaluated libraries, and the IAEA standards.
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| 6. |
- Paradela, C., et al.
(författare)
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High-accuracy determination of the 238U/235U fission cross section ratio up to ~1 GeV at n_TOF at CERN
- 2015
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 91, s. 024602-
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Tidskriftsartikel (refereegranskat)abstract
- The U238 to U235 fission cross section ratio has been determined at n_TOF up to ≈1 GeV, with two different detection systems, in different geometrical configurations. A total of four datasets has been collected and compared. They are all consistent to each other within the relative systematic uncertainty of 3–4%. The data collected at n_TOF have been suitably combined to yield a unique fission cross section ratio as a function of neutron energy. The result confirms current evaluations up to 200 MeV. Good agreement is also observed with theoretical calculations based on the INCL++/Gemini++ combination up to the highest measured energy. The n_TOF results may help solve a long-standing discrepancy between the two most important experimental datasets available so far above 20 MeV, while extending the neutron energy range for the first time up to ≈1 GeV.
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| 7. |
- Baykov, Vitaly, et al.
(författare)
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Ab Initio Studies of the Energy Characteristics and Magnetic Properties of Point Defects in GaAs
- 2005
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Ingår i: Physics of the solid state. - : Pleiades Publishing Ltd. - 1063-7834 .- 1090-6460. ; 47:10, s. 1831-1836
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Tidskriftsartikel (refereegranskat)abstract
- The formation energies of intrinsic point defects and solution energies of transition metal impurities in gallium arsenide are determined on the basis of ab initio calculations using the method of a locally self-consistent Green's function, which is a generalization of the coherent potential approximation. Based on the calculated energies, the conclusion is made that the As-Ga antisite defect is the most common intrinsic defect in GaAs. Calculations showed that transition metal impurities, except for Ni, preferentially occupy gallium sites substitutionally. The magnetic moments of impurity atoms are calculated as a function of the chemical environment. It is shown that, in compensated GaAs, Mn atoms tend to form clusters.
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| 8. |
- Paradela, C., et al.
(författare)
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High accuracy 235U(n,f) data in the resonance energy region
- 2016
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Ingår i: EPJ Web of Conferences. - : EDP Sciences. - 2100-014X.
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Konferensbidrag (refereegranskat)abstract
- The U-235 neutron-induced cross section is widely used as reference cross section for measuring other fission cross sections, but in the resonance region it is not considered as an IAEA standard because of the scarce experimental data covering the full region. In this work, we deal with a new analysis of the experimental data obtained with a detection setup based on parallel plate ionization chambers (PPACs) at the CERN n_TOF facility in the range from 1 eV to 10 keV. The relative cross section has been normalised to the IAEA value in the region between 7.8 and 11 eV, which is claimed as well-known. Comparison with the ENDF/B-VII evaluation and the IAEA reference file from 100 eV to 10 keV are provided.
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| 9. |
- Abbondanno, U, et al.
(författare)
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The data acquisition system of the neutron time-of-flight facility n_TOF at CERN
- 2005
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 538:1-3, s. 692-702
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Tidskriftsartikel (refereegranskat)abstract
- The n_TOF facility at CERN has been designed for the measurement of neutron capture, fission and (n, xn) cross-sections with high accuracy. This requires a flexible and-due to the high instantaneous neutron flux-almost dead time free data acquisition system. A scalable and versatile data solution has been designed based on 8-bit flash-ADCs with sampling rates up to 2 GHz and 8 Mbyte memory buffer. The software is written in C and C++ and is running on PCs equipped with RedHat Linux.
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| 10. |
- Bleskov, I. D., et al.
(författare)
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Ab initio calculations of elastic properties of Ru1-xNixAl superalloys
- 2009
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 94:16
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio total energy calculations based on the exact muffin-tin orbitals method, combined with the coherent potential approximation, have been used to study the thermodynamical and elastic properties of substitutional refractory Ru1-xNixAl alloys. We have found that the elastic constants C' and C11 exhibit pronounced peculiarities near the concentration of about 40 at. % Ni, which we ascribe to electronic topological transitions. Our suggestion is supported by the Fermi surface calculations in the whole concentration range. Results of our calculations show that one can design Ru-Ni-Al alloys substituting Ru by Ni (up to 40 at. %) with almost invariable elastic constants and reduced density.
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