| 1. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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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. |
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| 4. |
- Ala-Laurinaho, J., et al.
(författare)
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TUMESA - MEMS tuneable metamaterials for smart wireless applications
- 2012
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Ingår i: European Microwave Week 2012: "Space for Microwaves", EuMW 2012, Conference Proceedings - 7th European Microwave Integrated Circuits Conference, EuMIC 2012. - : IEEE. - 9782874870286 ; , s. 95-98
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Konferensbidrag (refereegranskat)abstract
- This paper describes the main results of the EU FP7 project TUMESA - MEMS tuneable metamaterials for smart wireless applications. In this project, we studied several reconfigurable antenna approaches that combine the new technology of MEMS with the new concept of artificial electromagnetic materials and surfaces (metamaterials and metasurfaces) for realisation of millimetre wave phase shifters and beam-steering devices. MEMS technology allows to miniaturise electronic components, reduce their cost in batch production, and effectively compete with semiconductor and ferroelectric based technologies in terms of losses at millimetre wavelengths. Novel tuneable materials and components proposed in this project perform as smart beam steering devices. Fabricated with MEMS technology in batch and on a single chip, proposed tuneable devices allow substituting of larger and more complex sub-system of, e.g., a radar sensor. This substitution provides a dramatic cost reduction on a system level.
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| 5. |
- 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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| 6. |
- 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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| 7. |
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| 8. |
- Herbst, SA, et al.
(författare)
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Proteogenomics refines the molecular classification of chronic lymphocytic leukemia
- 2022
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 6226-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer heterogeneity at the proteome level may explain differences in therapy response and prognosis beyond the currently established genomic and transcriptomic-based diagnostics. The relevance of proteomics for disease classifications remains to be established in clinically heterogeneous cancer entities such as chronic lymphocytic leukemia (CLL). Here, we characterize the proteome and transcriptome alongside genetic and ex-vivo drug response profiling in a clinically annotated CLL discovery cohort (n = 68). Unsupervised clustering of the proteome data reveals six subgroups. Five of these proteomic groups are associated with genetic features, while one group is only detectable at the proteome level. This new group is characterized by accelerated disease progression, high spliceosomal protein abundances associated with aberrant splicing, and low B cell receptor signaling protein abundances (ASB-CLL). Classifiers developed to identify ASB-CLL based on its characteristic proteome or splicing signature in two independent cohorts (n = 165, n = 169) confirm that ASB-CLL comprises about 20% of CLL patients. The inferior overall survival in ASB-CLL is also independent of both TP53- and IGHV mutation status. Our multi-omics analysis refines the classification of CLL and highlights the potential of proteomics to improve cancer patient stratification beyond genetic and transcriptomic profiling.
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| 9. |
- Campion, James, 1989-, et al.
(författare)
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Toward Industrial Exploitation of THz Frequencies : Integration of SiGe MMICs in Silicon-Micromachined Waveguide Systems
- 2019
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Ingår i: IEEE Transactions on Terahertz Science and Technology. - : Institute of Electrical and Electronics Engineers (IEEE). - 2156-342X .- 2156-3446. ; 9:6, s. 624-636
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Tidskriftsartikel (refereegranskat)abstract
- A new integration concept for terahertz (THz) systems is presented in this article, wherein patterned silicon-on-insulator wafers form all DC, IF, and RF networks in a homogeneous medium, in contrast to existing solutions. Using this concept, silicon-micromachined waveguides are combined with silicon germanium (SiGe) monolithic microwave integrated circuits (MMICs) for the first time. All features of the integration platform lie in the waveguide’s H-plane. Heterogeneous integration of SiGe chips is achieved using a novel in-line H-plane transition. As an initial step toward complete systems, we outline the design, fabrication, and assembly of back-to-back transition structures, for use at D-band frequencies (110ï¿œ170 GHz). Special focus is given to the industrial compatibility of all components, fabrication, and assembly processes, with an eye on the future commercialization of THz systems. Prototype devices are assembled via two distinct processes, one of which utilizes semiautomated die-bonding tools. Positional and orientation tolerances for each process are quantified. An accuracy of $\pm \text3.5\; μ \textm$, $\pm \text1.5 °$ is achieved. Measured $S$-parameters for each device are presented. The insertion loss of a single-ended transition, largely due to MMIC substrate losses, is 4.2ï¿œ5.5 dB, with a bandwidth of 25 GHz (135ï¿œ160 GHz). Return loss is in excess of 5 dB. Measurements confirm the excellent repeatability of the fabrication and assembly processes and, thus, their suitability for use in high-volume applications. The proposed integration concept is highly scalable, permitting its usage far into the THz frequency spectrum. This article represents the first stage in the shift to highly compact, low-cost, volume-manufacturable THz waveguide systems.
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| 10. |
- Hussain, T., et al.
(författare)
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Superior sensing affinities of acetone towards vacancy induced and metallized ZnO monolayers
- 2018
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Ingår i: Applied Surface Science. - : ELSEVIER SCIENCE BV. - 0169-4332 .- 1873-5584. ; 456, s. 711-716
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Tidskriftsartikel (refereegranskat)abstract
- The sensing propensities of acetone molecule towards zinc oxide monolayers (ZnO-ML) have been studied by means of density functional theory (DFT) calculations. Our van der Waals induced first principles calculations revealed that pristine ZnO-ML barely binds acetone, which limits its application as acetone sensing materials. However the formation of vacancies and foreign element doping improves acetone binding drastically. Among several defects, divacancy, and metal doping Li, Sc and Ti functionalization on ZnO-ML has been found the most promising ones. Presence of dangling electrons and partial positive charges in case of vacancy-induced and metallized ZnO-ML respectively, is believed to enhance the binding of acetone on the monolayers. The acetone-ZnO binding behavior has been further explained through studying the electronic properties by density of states and charge transfer mechanism though Bader analysis. Thus defected and metallized ZnO-ML could be a promising nano sensor for efficient sensing/capture of acetone.
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