| 1. |
- 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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| 5. |
- Yuan, X., et al.
(author)
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Prognostic value of amplitude-integrated EEG in neonates with high risk of neurological sequelae
- 2020
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In: Annals of Clinical and Translational Neurology. - : Wiley. - 2328-9503. ; 7:2, s. 210-218
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Journal article (peer-reviewed)abstract
- Objective To determine the efficacy and the prognostic value of amplitude-integrated electroencephalography (aEEG) in term and near-term neonates with high risk of neurological sequelae. Methods Infants of >= 35 weeks of gestation diagnosed with neonatal encephalopathy or with high risk of brain injury were included. All eligible infants underwent aEEG within 6 h after clinical assessment. The infants were followed up 12 months to evaluate neurological development. Results A total of 250 infants were eligible, of which 85 had normal aEEG, 81 had mildly abnormal aEEG, and 84 had severely abnormal aEEG. Of these infants, 168 were diagnosed with different neonatal encephalopathies, 27 with congenital or metabolic diseases, and 55 with high risk of brain injury. In all, 22 infants died, 19 were lost to follow-up, and 209 completed the follow-up at 12 months, of which 62 were diagnosed with a neurological disability. Statistical analysis showed that severely abnormal aEEG predicted adverse neurological outcome with a sensitivity of 70.2%, a specificity of 87.1%, a positive predictive value of 75.6%, and a negative predictive value of 83.7%. Interpretation aEEG can predict adverse outcomes in high-risk neonates and is a useful method for monitoring neonates with high risk of adverse neurological outcomes.
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| 6. |
- Zhang, Y., et al.
(author)
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Submarine groundwater discharge drives coastal water quality and nutrient budgets at small and large scales
- 2020
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In: Geochimica et Cosmochimica Acta. - : Elsevier BV. - 0016-7037. ; 290, s. 201-215
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Journal article (peer-reviewed)abstract
- Submarine groundwater discharge (SGD) can be a significant source of chemical pollutants from land to ocean. Here, we first estimated SGD using radium isotopes and related nutrient fluxes at the local scale in Jiaozhou Bay (JZB), a typical Chinese system that is experiencing rapid urban and industrial development. We then summarized SGDstudies off China to assess the largescale implications of SGD to nutrient budgets. In JZB, the location of contaminated nearshore waters revealed by an integrative water quality index (WQI) coincided with the SGD hotspots. The total (fresh and saline) SGD flux in JZB was estimated to be (0.64-1.67) x 10(7) m(3)/d or (2.12-5.59) cm/d based on Ra-224 and Ra-228 mass balance models. This was approximately 8 times the discharge rate of local rivers. By combining these JZB results with the literature data, we provide the first estimate of SGD and associated nutrient fluxes off China. The magnitude of SGD at the China-scale was (5.40-10.2) x 10(12) m(3)/yr, accounting for 59% of the global SGD flux. SGD-derived nutrient fluxes summarized from similar to 40 previous studies were one order of magnitude higher than riverine inputs. These nutrients fluxes from SGD contributed >50% of the total dissolved inorganic nitrogen (DIN), phosphorous (DIP) and silicate (DSi) inputs into Chinese coastal waters, which can explain about 60% of the phosphorus required by primary production. The mean DIN/DIP ratio (121) in SGD was significantly higher than the Redfield ratio, with important implications for phytoplankton growth and structure. SGD can influence water quality, dominate nutrient budgets, and drive primary production not only at the local scale, but also at the regional and global scales.
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| 7. |
- Bakker, M. K., et al.
(author)
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Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors
- 2020
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 52:12
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Journal article (peer-reviewed)abstract
- Rupture of an intracranial aneurysm leads to subarachnoid hemorrhage, a severe type of stroke. To discover new risk loci and the genetic architecture of intracranial aneurysms, we performed a cross-ancestry, genome-wide association study in 10,754 cases and 306,882 controls of European and East Asian ancestry. We discovered 17 risk loci, 11 of which are new. We reveal a polygenic architecture and explain over half of the disease heritability. We show a high genetic correlation between ruptured and unruptured intracranial aneurysms. We also find a suggestive role for endothelial cells by using gene mapping and heritability enrichment. Drug-target enrichment shows pleiotropy between intracranial aneurysms and antiepileptic and sex hormone drugs, providing insights into intracranial aneurysm pathophysiology. Finally, genetic risks for smoking and high blood pressure, the two main clinical risk factors, play important roles in intracranial aneurysm risk, and drive most of the genetic correlation between intracranial aneurysms and other cerebrovascular traits. Cross-ancestry genome-wide association analyses in individuals of European and East Asian ancestry identify 11 new risk loci for intracranial aneurysms and highlight a polygenic architecture explaining a substantial fraction of disease heritability.
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- Guo, S., et al.
(author)
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Evidence for pseudospin-chiral quartet bands in the presence of octupole correlations
- 2020
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In: Physics Letters B. - : ELSEVIER. - 0370-2693 .- 1873-2445. ; 807
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Journal article (peer-reviewed)abstract
- Three nearly degenerate pairs of doublet bands are identified in Ba-131. Two of them, with positive-parity, are interpreted as pseudospin-chiral quartet bands. This is the first time that a complete set of chiral doublet bands built on the pseudospin partners pi(d(5/2), g(7/2)) is observed. The chiral bands with opposite parity built on 3-quasiparticle configurations are directly connected by many E1 transitions, without involving an intermediary non-chiral configuration. The observed band structures in Ba-131 have been investigated by using the reflection-asymmetric particle rotor model. The energies and the electromagnetic transition ratios of the three pairs of doublet bands observed in Ba-131 are reproduced and they are interpreted as chiral doublet bands with three-quasiparticle configurations. It is the first time that multiple chiral bands are observed in the presence of enhanced octupole correlations and pseudospin symmetry.
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| 9. |
- Kinyoki, DK, et al.
(author)
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Mapping child growth failure across low- and middle-income countries
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 577:7789, s. 231-
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Journal article (peer-reviewed)abstract
- Childhood malnutrition is associated with high morbidity and mortality globally1. Undernourished children are more likely to experience cognitive, physical, and metabolic developmental impairments that can lead to later cardiovascular disease, reduced intellectual ability and school attainment, and reduced economic productivity in adulthood2. Child growth failure (CGF), expressed as stunting, wasting, and underweight in children under five years of age (0–59 months), is a specific subset of undernutrition characterized by insufficient height or weight against age-specific growth reference standards3–5. The prevalence of stunting, wasting, or underweight in children under five is the proportion of children with a height-for-age, weight-for-height, or weight-for-age z-score, respectively, that is more than two standard deviations below the World Health Organization’s median growth reference standards for a healthy population6. Subnational estimates of CGF report substantial heterogeneity within countries, but are available primarily at the first administrative level (for example, states or provinces)7; the uneven geographical distribution of CGF has motivated further calls for assessments that can match the local scale of many public health programmes8. Building from our previous work mapping CGF in Africa9, here we provide the first, to our knowledge, mapped high-spatial-resolution estimates of CGF indicators from 2000 to 2017 across 105 low- and middle-income countries (LMICs), where 99% of affected children live1, aggregated to policy-relevant first and second (for example, districts or counties) administrative-level units and national levels. Despite remarkable declines over the study period, many LMICs remain far from the ambitious World Health Organization Global Nutrition Targets to reduce stunting by 40% and wasting to less than 5% by 2025. Large disparities in prevalence and progress exist across and within countries; our maps identify high-prevalence areas even within nations otherwise succeeding in reducing overall CGF prevalence. By highlighting where the highest-need populations reside, these geospatial estimates can support policy-makers in planning interventions that are adapted locally and in efficiently directing resources towards reducing CGF and its health implications.
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