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- 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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| 5. |
- Callaway, EM, et al.
(författare)
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A multimodal cell census and atlas of the mammalian primary motor cortex
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
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Tidskriftsartikel (refereegranskat)abstract
- Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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- Li, G, et al.
(författare)
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Developing a Core Outcome Set for Clinical Trials of Chinese Medicine for Hyperlipidemia
- 2022
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Ingår i: Frontiers in pharmacology. - : Frontiers Media SA. - 1663-9812. ; 13, s. 847101-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Chinese medicine (CM) is widely used for treating hyperlipidemias, especially in China. However, the heterogeneity of outcomes measured and reported across trials exacerbates the obstacles of evidence synthesis and effectiveness comparison. In this study, we develop a core outcome set (COS) for CM clinical trials for hyperlipidemia (COS-CM-Hyperlipidemia) to tackle the outcome issues.Methods: We generated candidate outcomes through a systematic review of interventional and observational studies of Chinese medicine for hyperlipidemias. The comprehensive search strategy was employed. Study selection and data collection were independently done by two researchers. We searched clinical trial registry platform to supplement the outcomes list extracted by systematic review. Then, we conducted a three-round Delphi survey. The stakeholders were hyperlipidemia patients, clinicians or researchers, in either CM/integrated Chinese or Western medicine, clinical pharmacy, clinical epidemiology or statisticians, or editors of important relevant journals and an ethicist. They used a 9-point Likert scale to determine how important they felt each outcome was in determining treatment success. A consensus meeting was held to confirm the final COS, based on the Delphi survey results.Results: We identified a total of 433 outcomes from 3,547 articles, and 28 outcomes from 367 registered trials. After standardization, we selected 71 outcomes to develop a preliminary outcome list for further consensus. After three Delphi survey rounds and one consensus meeting, the most important outcomes were determined for COS-CM-Hyperlipidemia. It included cardiovascular events, low-density lipoprotein cholesterol, risk of cardiovascular disease, total cholesterol, carotid intima-media thickness, high-density lipoprotein cholesterol, triglycerides, cerebrovascular events, adverse drug reactions and patient-reported symptoms.Conclusion: COS-CM-Hyperlipidemia may improve outcome reporting consistency in clinical trials. Further work is needed to explore the optimal methods for measuring these outcomes.Registration: The Core Outcome Measures in Effectiveness Trials Initiative (COMET): http://www.cometinitiative.org/studies/details/983. Registered on 25 April 2017.
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| 9. |
- Li, G, et al.
(författare)
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Outcome Reporting Variability in Trials of Chinese Medicine for Hyperlipidemia: A Systematic Review for Developing a Core Outcome Set
- 2021
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Ingår i: Evidence-based complementary and alternative medicine : eCAM. - : Hindawi Limited. - 1741-427X .- 1741-4288. ; 2021, s. 8822215-
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Tidskriftsartikel (refereegranskat)abstract
- Introduction. Hyperlipidemia is an underlying process behind cardiovascular disease. Chinese medicine (CM) may be effective in treating hyperlipidemia, but there is a lack of studies with high methodological quality. A major reason for this is heterogeneity in outcome reporting. Therefore, this study explores the degree of outcome reporting variation in CM trials for hyperlipidemia. It then generates a list of potentially important outcomes for developing a core outcome set (COS). Methods. A systematic review of literature focusing on studies of CM for hyperlipidemia was conducted. Outcomes were listed verbatim and grouped into 8 domains. Outcome frequency and definition uniformity were analyzed. Results. 3,702 studies and 452 individual outcomes were identified. These outcomes were reported 27,328 times, of which 1.6% were reported as primary outcomes, and 13.3% were defined. The most frequent outcome was total triglyceride, represented in 86.7% of the studies, followed by total cholesterol (86.0%), total effective rate (75.1%), high-density lipoprotein cholesterol (73.2%), and low-density lipoprotein cholesterol (60.5%). However, 43.6% of outcomes were reported only once. The largest outcome domain was “pathological or pathophysiological outcomes,” which included 67.0% of outcomes. Of the “response rate related outcomes” domain, total effective rate was the most frequently reported outcome (n = 2,780), and 95.3% of the studies gave a clear definition. However, these definitions were often contradictory. Only 10 papers reported cardiovascular events, 3 of which referred to them as primary outcomes. Moreover, ten patient-reported outcomes were reported in the retrieved literature 19 times in total. The majority of the outcomes did not report measurement instruments (MIs) (269/453, 59.4%). MIs of the surrogate outcomes were reported more frequently. Conclusion. Outcome reporting in CM trials for hyperlipidemia is inconsistent and ill-defined, creating barriers to data synthesis and comparison. Thus, we propose and are developing a COS for CM trials for hyperlipidemia.
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