| 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. |
- Discepola, MN, et al.
(författare)
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Effects of non-pharmacological and non-surgical interventions on health outcomes in systemic sclerosis: protocol for a living systematic review
- 2021
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Ingår i: BMJ open. - : BMJ. - 2044-6055. ; 11:5, s. e047428-
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Tidskriftsartikel (refereegranskat)abstract
- Systemic sclerosis (SSc; scleroderma) is a rare, chronic, autoimmune disease with a high level of burden, a significant impact on the ability to carry out daily activities, and a considerable negative impact on health-related quality of life. Non-pharmacological interventions could be provided to potentially improve mental and physical health outcomes. However, the effectiveness of non-pharmacological interventions on health and well-being among individuals with SSc has not been well established. The proposed living systematic review aims to identify and evaluate randomised controlled trial (RCT) evidence on the effectiveness of non-pharmacological and non-surgical interventions on mental and physical health outcomes and on the delivery of such services in SSc.Methods and analysisEligible studies will be RCTs that examine non-pharmacological and non-surgical interventions aimed at improving health outcomes among individuals with SSc or the delivery of services intended to improve healthcare or support of people with SSc (eg, support groups). All RCTs included in a previous systematic review that sought studies published between 1990 and March 2014 will be evaluated for inclusion. Additional trials will be sought from January 2014 onwards using a similar, augmented search strategy developed by a health sciences librarian. We will search the MEDLINE, Embase, CINAHL, PsycINFO, Cochrane Library and Web of Science databases and will not restrict by language. Two independent reviewers will determine the eligibility of identified RCTs and will extract data using a prespecified standardised form in DistillerSR. Meta-analyses will be considered if ≥2 eligible RCTs report similar non-pharmacological interventions and comparable health outcomes. We will conduct a qualitative synthesis for interventions that cannot be synthesised via meta-analysis.Ethics and disseminationWe will post initial and ongoing results via a website, publish results periodically via peer-reviewed journal publication, and present results at patient-oriented events.PROSPERO registration numberCRD42020219914.
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| 3. |
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| 4. |
- Yakneen, S, et al.
(författare)
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Butler enables rapid cloud-based analysis of thousands of human genomes
- 2020
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Ingår i: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 38:3, s. 288-
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Tidskriftsartikel (refereegranskat)abstract
- We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data processing and analysis by 43% compared with current approaches. Butler enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform manner.
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| 5. |
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| 6. |
- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 7. |
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