| 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. |
- Jacobsson, Jesper, 1984-, et al.
(författare)
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An open-access database and analysis tool for perovskite solar cells based on the FAIR data principles
- 2022
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Ingår i: Nature Energy. - : Springer Nature. - 2058-7546. ; 7:1, s. 107-115
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Tidskriftsartikel (refereegranskat)abstract
- Large datasets are now ubiquitous as technology enables higher-throughput experiments, but rarely can a research field truly benefit from the research data generated due to inconsistent formatting, undocumented storage or improper dissemination. Here we extract all the meaningful device data from peer-reviewed papers on metal-halide perovskite solar cells published so far and make them available in a database. We collect data from over 42,400 photovoltaic devices with up to 100 parameters per device. We then develop open-source and accessible procedures to analyse the data, providing examples of insights that can be gleaned from the analysis of a large dataset. The database, graphics and analysis tools are made available to the community and will continue to evolve as an open-source initiative. This approach of extensively capturing the progress of an entire field, including sorting, interactive exploration and graphical representation of the data, will be applicable to many fields in materials science, engineering and biosciences.
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| 3. |
- 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. |
- Paramasivam, Abinethaa, et al.
(författare)
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The International Classification of Functioning, Disability and Health Core Set for deafblindness. Part I : a systematic review of outcome measures
- 2023
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Ingår i: European Journal of Physical and Rehabilitation Medicine. - : Edizioni Minerva Medica. - 1973-9087 .- 1973-9095. ; 59:5, s. 615-627
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Forskningsöversikt (refereegranskat)abstract
- INTRODUCTION: The International Classification of Functioning, Disability, and Health (ICF), developed by the World Health Organization, is a classification framework that focuses on the health and functioning of people with disabilities. As part of an ICF Core Set development, four studies need to be conducted, one of which is a systematic review. This study presents part 1 of the systematic review that aims to describe the outcome measures identified in the literature related to functioning in individuals with deafblindness. EVIDENCE ACQUISITION: The research team screened articles from eight scientific databases, three journals, and Google Scholar (March 2011 to September 2022). Articles were included if they studied individuals with deafblindness aged 18 and older. Studies that examined genetics or laboratory experiments involving animals were excluded. Data were extracted into a logbook with key descriptors such as study location and design, age of study population, and instruments/outcome measures used, which were further categorized into one of the following types: 1) standardized; 2) patient-reported measures, standardized (PT-S); 3) patient-reported measures, not standardized (PT-not S); 4) health professional, reported measures, standardized (HP-S); 5) Technical measures; 6) other measures (parent-reported standardized and laboratory measures).EVIDENCE SYNTHESIS: The review included 147 studies, of which most were conducted in Europe (47.6%) and North America (27.9%). Of the 314 identified outcome measures, 57 were Standardized, 59 were Patient Reported-Standardized (PT-S), 178 were patient reported non-standardized (PT-Not S) variables, 11 were health professional reported, standardized, five were technical, and four were classified as other measures.CONCLUSIONS: Most instruments measured functioning in daily activities and the mental health of individuals with deafblindness. Three deafblind-specific instruments were identified in this study, highlighting the need for more deafblind-specific instruments to be developed and utilized in research.
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