| 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. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 3. |
- Nilsson, Thomas, 1965, et al.
(författare)
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Neutron Momentum Distributions from Core Break-up Reactions of Halo Nuclei
- 1995
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Ingår i: Europhysics Letters. - 0295-5075 .- 1286-4854. ; 30:1, s. 19-24
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Tidskriftsartikel (refereegranskat)abstract
- Neutron angular distributions from violent break-up reactions of Li-11 and Be-11 have been measured at 28 MeV/u and 280 MeV/u and at 41 MeV/u and 460 MeV/u, respectively. The derived neutron momentum distributions show a narrow component in transverse momentum that is within uncertainties independent of beam energy and target charge. This component is suggested to be simply related to the momentum distribution of the loosely bound halo neutron(s) in the projectiles.
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| 4. |
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| 5. |
- Anne, R., et al.
(författare)
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Dissociation Reactions of the Be-11 One-Neutron Halo - the Interplay between Structure and Reaction-Mechanism
- 1993
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Ingår i: Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 304:1-2, s. 55-59
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Tidskriftsartikel (refereegranskat)abstract
- The angular distributions of the forward neutrons in the exclusive (Be-10 + n) channel have been measured. They can be accounted for quantitatively and without free parameters in terms of Coulomb and diffraction dissociation. The results show that the transverse momentum distributions result from an interplay between the tail of the wave function (the halo) and the reaction mechanism.
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| 6. |
- Bergmann, U. C., et al.
(författare)
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On the beta-decay of C-9
- 2001
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Ingår i: Nuclear Physics A. - 0375-9474. ; 692:3-4, s. 427-450
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Tidskriftsartikel (refereegranskat)abstract
- In beta -decay experiments on C-9 at CERN/ISOLDE the beta -strength was determined to the ground state, the 12.2 MeV excited state and the Isobaric Analog State (IAS) at 14.655 MeV in B-9. A large beta -strength asymmetry is deduced for the mirror transitions of C-9 and Li-9 to states around 12 MeV excitation energy. A satisfactory description of the three-body decay from a narrow energy region around the 12.2 MeV resonance is obtained within a sequential model involving the ground and first-excited states of Li-5 and Be-8. From the study of angular correlations the spin of the 12.2 MeV state is determined as 5/2(-). For the first time the population of the IAS is observed in beta -decay and new information on the decay of this state is obtained. The advantages of a closely packed. highly segmented detector setup are demonstrated. (C) 2001 Elsevier Science B.V. All rights reserved.
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| 7. |
- 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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| 8. |
- Keller, H., et al.
(författare)
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Search for Forbidden Beta-Decays of the Drip-Line Nucleus Be-12
- 1994
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Ingår i: Zeitschrift fur Physik A Hadrons and Nuclei. - 1431-5831 .- 0939-7922. ; 348:1, s. 61-62
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Tidskriftsartikel (refereegranskat)abstract
- Beta-coincident gamma-rays have been measured from implanted pure samples of Be-12 separated at the LISE3 spectrometer at GANIL. An intensity of 0.040(26)% can be estimated for the branching ratio of the isospin forbidden pure-Fermi transition to the 0+ excited state of B-12 and of 0.008(6) % of the transition to the 1- excited state. Both are taken to represent upper limits. The halflife has been re-measured to be 26.1(2.4) ms.
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| 9. |
- 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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| 10. |
- Anne, R., et al.
(författare)
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Exclusive and Restricted-Inclusive Reactions Involving the Be-11 One-Neutron Halo
- 1994
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Ingår i: Nuclear Physics A. - : Elsevier BV. - 0375-9474. ; 575:1, s. 125-154
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Tidskriftsartikel (refereegranskat)abstract
- Reactions of a 41 MeV/u beam of the radioactive halo nucleus Be-11 have been studied with a counter telescope coupled to an array of neutron detectors covering angles up to 97-degrees. The technique allows to determine single-neutron inclusive and exclusive angular distributions. The targets (Be, Ti and Au) were chosen to illustrate the relative roles played by nuclear and Coulomb mechanisms. The channels leading to Be-10, the dissociation channels, correspond to impact parameters larger than the sum of the radii of the target and the Be-10 core. It is shown that for the dissociation process it is possible to account almost quantitatively for the integral, single- and double-differential cross sections from models without free parameters including the Coulomb, Serber and Glauber (diffraction-dissociation) mechanisms. The neutron distributions from the nondissociative reaction channels show little individuality and it is convenient to group them together as the channel ''neutron plus anything different from Be-10''. We refer to these as ''restricted-inclusive'' reactions. These seem to be a promising tool for obtaining accurate information on the halo wave function in momentum coordinates.
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