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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. |
- Menzel, Annette, et al.
(författare)
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European phenological response to climate change matches the warming pattern
- 2006
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Ingår i: Global Change Biology. - 1354-1013 .- 1365-2486. ; 12:10, s. 1969-1976
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Tidskriftsartikel (refereegranskat)abstract
- Global climate change impacts can already be tracked in many physical and biological systems; in particular, terrestrial ecosystems provide a consistent picture of observed changes. One of the preferred indicators is phenology, the science of natural recurring events, as their recorded dates provide a high-temporal resolution of ongoing changes. Thus, numerous analyses have demonstrated an earlier onset of spring events for mid and higher latitudes and a lengthening of the growing season. However, published single-site or single-species studies are particularly open to suspicion of being biased towards predominantly reporting climate change-induced impacts. No comprehensive study or meta-analysis has so far examined the possible lack of evidence for changes or shifts at sites where no temperature change is observed. We used an enormous systematic phenological network data set of more than 125000 observational series of 542 plant and 19 animal species in 21 European countries (1971-2000). Our results showed that 78% of all leafing, flowering and fruiting records advanced (30% significantly) and only 3% were significantly delayed, whereas the signal of leaf colouring/fall is ambiguous. We conclude that previously published results of phenological changes were not biased by reporting or publication predisposition: the average advance of spring/summer was 2.5 days decade -1 in Europe. Our analysis of 254 mean national time series undoubtedly demonstrates that species' phenology is responsive to temperature of the preceding months (mean advance of spring/summer by 2.5 days °C -1, delay of leaf colouring and fall by 1.0 day °C -1). The pattern of observed change in spring efficiently matches measured national warming across 19 European countries (correlation coefficient r = -0.69, P < 0.001).
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| 4. |
- Sikoparija, B., et al.
(författare)
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Spatial and temporal variations in airborne Ambrosia pollen in Europe
- 2017
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Ingår i: Aerobiologia. - : Springer Science and Business Media LLC. - 0393-5965 .- 1573-3025. ; 33, s. 181-189
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Tidskriftsartikel (refereegranskat)abstract
- © 2016, The Author(s). The European Commission Cooperation in Science and Technology (COST) Action FA1203 “SMARTER” aims to make recommendations for the sustainable management of Ambrosia across Europe and for monitoring its efficiency and cost-effectiveness. The goal of the present study is to provide a baseline for spatial and temporal variations in airborne Ambrosia pollen in Europe that can be used for the management and evaluation of this noxious plant. The study covers the full range of Ambrosia artemisiifolia L. distribution over Europe (39°N–60°N; 2°W–45°E). Airborne Ambrosia pollen data for the principal flowering period of Ambrosia (August–September) recorded during a 10-year period (2004–2013) were obtained from 242 monitoring sites. The mean sum of daily average airborne Ambrosia pollen and the number of days that Ambrosia pollen was recorded in the air were analysed. The mean and standard deviation (SD) were calculated regardless of the number of years included in the study period, while trends are based on those time series with 8 or more years of data. Trends were considered significant at p<0.05. There were few significant trends in the magnitude and frequency of atmospheric Ambrosia pollen (only 8% for the mean sum of daily average Ambrosia pollen concentrations and 14% for the mean number of days Ambrosia pollen were recorded in the air). The direction of any trends varied locally and reflected changes in sources of the pollen, either in size or in distance from the monitoring station. Pollen monitoring is important for providing an early warning of the expansion of this invasive and noxious plant.
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| 7. |
- Li, Constance H., et al.
(författare)
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Sex differences in oncogenic mutational processes
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
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| 9. |
- Merheb, J., et al.
(författare)
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Influence of Skeletal and Local Bone Density on Dental Implant Stability in Patients with Osteoporosis
- 2016
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Ingår i: Clinical Implant Dentistry and Related Research. - : Wiley. - 1523-0899 .- 1708-8208. ; 18:2, s. 253-260
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Tidskriftsartikel (refereegranskat)abstract
- Background and PurposeOsteoporosis is a major skeletal disease affecting millions of people worldwide. Recent studies claim that patients with osteoporosis do not have a higher risk of early implant failure compared to non-osteoporotic patients. The aim of this study was to assess the effect of skeletal osteoporosis and local bone density on initial dental implant stability. Materials and MethodsSeventy-three patients were recruited and were assigned (based on a Dual-energy X-ray Absorptiometry scan) to either the osteoporosis (Opr), osteopenia (Opn), or control (C) group. Forty nine of the 73 patients received dental implants and had implant stability measured by means of resonance frequency analysis (RFA) at implant placement and at prosthetic abutment placement. On the computerized tomography scans, the cortical thickness and the bone density (Hounsfield Units) at the sites of implant placement were measured. ResultsAt implant placement, primary stability was on average lower in group Opr (63.310.3 ISQ) than in group Opn (65.3 +/- 7.5 implant stability qutient (ISQ)), and group C (66.7 +/- 8.7 ISQ). At abutment placement, a similar trend was observed: group Opr (66.4 +/- 9.5 ISQ) scored lower than group Opn (70.7 +/- 7.8 ISQ), while the highest average was for group C (72.2 +/- 7.2 ISQ). The difference between groups Opr and C was significant. Implant length and diameter did not have a significant effect on implant stability as measured with RFA. A significant correlation was found between local bone density and implant stability for all regions of interest. ConclusionsImplant stability seems to be influenced by both local and skeletal bone densities. The lower stability scores in patient with skeletal osteoporosis reinforce the recommendations that safe protocols and longer healing times could be recommended when treating those patients with dental implants.
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| 10. |
- Merheb, J., et al.
(författare)
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Relation between Spongy Bone Density in the Maxilla and Skeletal Bone Density
- 2015
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Ingår i: Clinical Implant Dentistry and Related Research. - : Wiley. - 1523-0899 .- 1708-8208. ; 17:6, s. 1180-1187
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Tidskriftsartikel (refereegranskat)abstract
- © 2015 Wiley Periodicals, Inc. Background and Purpose: Osteoporosis is a disease affecting more than 300 million people worldwide and is responsible for numerous medical complications. This study aimed to investigate the relation between skeletal and maxillary bone density. Materials and Methods: Seventy-three patients were recruited and divided between group A (osteoporosis), group B (healthy, control), and group C (osteopenia) on the basis of a dual-energy x-ray absorptiomery (DXA) scan. These patients also received a CT scan on which bone density measurements were performed at five sites: maxilla midline, retromolar tuberosities, incisor, premolars, and molar regions. Results: The bone density was lower in osteoporotic patients compared with the control patients. The bone mineral density (BMD) of the tuberosities showed the strongest correlations with the BMD of the hip and the spine (respectively, r=0.50 and r=0.61). The midline region showed moderate correlations with the hip (r=0.47) and the spine (r=0.46). For potential implant sites, the correlations with the BMD of the hip and spine were, however, small to insignificant. Based on measurements of bone density of the maxilla, it was possible to predict if the patient was osteoporotic or not with a sensitivity of 65% and a specificity of 83%. Conclusions: The maxillary bone density of subjects with osteoporosis is significantly lower than that of healthy patients. Moreover, there is a direct correlation between the density of the skeleton and the density of some sites of the maxilla. Using measurements of maxillary bone density in order to predict skeletal bone density might be a useful tool for the screening of osteoporosis.
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