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- 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. |
- Robinson, N. A., et al.
(author)
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Applying genetic technologies to combat infectious diseases in aquaculture
- 2022
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In: Reviews in Aquaculture. - : Wiley. - 1753-5123 .- 1753-5131. ; 15:2, s. 491-535
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Journal article (peer-reviewed)abstract
- Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies—sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture. © 2022 The Authors. Reviews in Aquaculture published by John Wiley & Sons Australia, Ltd.
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| 6. |
- Betsou, F, et al.
(author)
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Standard PREanalytical Code Version 3.0
- 2018
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In: Biopreservation and biobanking. - : Mary Ann Liebert Inc. - 1947-5543 .- 1947-5535. ; 16:1, s. 9-12
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Journal article (peer-reviewed)
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| 7. |
- Heuschele, J., et al.
(author)
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The sex specific metabolic footprint of Oithona davisae
- 2016
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In: Journal of Sea Research. - : Elsevier BV. - 1385-1101. ; 117, s. 1-6
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Journal article (peer-reviewed)abstract
- In pelagic copepods, the group representing the highest animal abundances on earth, males and females have distinct morphological and behavioural differences. In several species female pheromones are known to facilitate the mate finding process, and copepod exudates induce changes in physiology and behaviour in several phytoplankton species. Here we tested whether the sexual dimorphism in morphology and behaviour is mirrored in the exudate composition of males and females. We find differences in the exudate composition, with females seemingly producing more compounds. While we were able to remove the sex pheromones from the water by filtration through reverse phase solid phase extraction columns, we were not able to recover the active pheromone from the solid phase. © 2016 Elsevier B.V.
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| 8. |
- Hylving, L, et al.
(author)
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The Role of Dominant Design in a Product Developing Firm's Digital Innovation
- 2012
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In: Journal of Information Technology Theory and Application. - 1552-6496 .- 1532-4516. ; 13:2, s. 5-
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Journal article (peer-reviewed)abstract
- Digital technology offers new options for product-developing firms. However, to reap the benefits of digital technology, firms need to handle the tensions between these options the institutionalized practices established over long periods of incremental innovation. We report on a twenty month intensive case study of a global automaker€™s efforts to innovate instrument clusters explore the influencing role of established innovation practices. We develop a conceptual model for understanding how digital technology shapes, is conditioned by, the dominant design of a product class. Our research contributes to the emerging literature of digital innovation offers lessons learned for established firms dealing with the contradictory logics of digitized products_x000D_
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| 10. |
- Peters, Susan, et al.
(author)
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Narrative review of occupational exposures and noncommunicable diseases
- 2024
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In: ANNALS OF WORK EXPOSURES AND HEALTH. - 2398-7308 .- 2398-7316. ; 68:6, s. 562-580
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Research review (peer-reviewed)abstract
- Objective Within the scope of the Exposome Project for Health and Occupational Research on applying the exposome concept to working life health, we aimed to provide a broad overview of the status of knowledge on occupational exposures and associated health effects across multiple noncommunicable diseases (NCDs) to help inform research priorities.Methods We conducted a narrative review of occupational risk factors that can be considered to have "consistent evidence for an association," or where there is "limited/inadequate evidence for an association" for 6 NCD groups: nonmalignant respiratory diseases; neurodegenerative diseases; cardiovascular/metabolic diseases; mental disorders; musculoskeletal diseases; and cancer. The assessment was done in expert sessions, primarily based on systematic reviews, supplemented with narrative reviews, reports, and original studies. Subsequently, knowledge gaps were identified, e.g. based on missing information on exposure-response relationships, gender differences, critical time-windows, interactions, and inadequate study quality.Results We identified over 200 occupational exposures with consistent or limited/inadequate evidence for associations with one or more of 60+ NCDs. Various exposures were identified as possible risk factors for multiple outcomes. Examples are diesel engine exhaust and cadmium, with consistent evidence for lung cancer, but limited/inadequate evidence for other cancer sites, respiratory, neurodegenerative, and cardiovascular diseases. Other examples are physically heavy work, shift work, and decision latitude/job control. For associations with limited/inadequate evidence, new studies are needed to confirm the association. For risk factors with consistent evidence, improvements in study design, exposure assessment, and case definition could lead to a better understanding of the association and help inform health-based threshold levels.Conclusions By providing an overview of knowledge gaps in the associations between occupational exposures and their health effects, our narrative review will help setting priorities in occupational health research. Future epidemiological studies should prioritize to include large sample sizes, assess exposures prior to disease onset, and quantify exposures. Potential sources of biases and confounding need to be identified and accounted for in both original studies and systematic reviews.
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