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  • 2015-2019  (3)
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  • 1
    Publication Date: 2015-01-16
    Description: COSMIC, the Catalogue Of Somatic Mutations In Cancer ( http://cancer.sanger.ac.uk ) is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Our latest release (v70; Aug 2014) describes 2 002 811 coding point mutations in over one million tumor samples and across most human genes. To emphasize depth of knowledge on known cancer genes, mutation information is curated manually from the scientific literature, allowing very precise definitions of disease types and patient details. Combination of almost 20 000 published studies gives substantial resolution of how mutations and phenotypes relate in human cancer, providing insights into the stratification of mutations and biomarkers across cancer patient populations. Conversely, our curation of cancer genomes (over 12 000) emphasizes knowledge breadth, driving discovery of unrecognized cancer-driving hotspots and molecular targets. Our high-resolution curation approach is globally unique, giving substantial insight into molecular biomarkers in human oncology. In addition, COSMIC also details more than six million noncoding mutations, 10 534 gene fusions, 61 299 genome rearrangements, 695 504 abnormal copy number segments and 60 119 787 abnormal expression variants. All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2017-04-12
    Description: Understanding soil organic carbon (SOC) sequestration is important to develop strategies to increase the SOC stock and, thereby, off-set some of the increases in atmospheric carbon dioxide. Although the capacity of soils to store SOC in a stable form is commonly attributed to the fine (clay + fine silt) fraction, the properties of the fine fraction that determine the SOC stabilisation capacity are poorly known. The aim of this study was to develop an improved model to estimate the SOC stabilisation capacity of Allophanic (Andisols) and non-Allophanic topsoils (0-15 cm) and, as a case study, to apply the model to predict the sequestration potential of pastoral soils across New Zealand. A quantile (90 th ) regression model, based on the specific surface area and extractable aluminium (pyrophosphate) content of soils, provided the best prediction of the upper limit of fine fraction carbon (FFC) (i.e. the stabilisation capacity), but with different coefficients for Allophanic and non-Allophanic soils. The carbon (C) saturation deficit was estimated as the difference between the stabilisation capacity of individual soils and their current C concentration. For long-term pastures, the mean saturation deficit of Allophanic soils (20.3 mg C g −1 ) was greater than that of non-Allophanic soils (16.3 mg C g −1 ). The saturation deficit of cropped soils was 1.14 to 1.89 times that of pasture soils. The sequestration potential of pasture soils ranged from 10 t C ha −1 (Ultic soils) to 42 t C ha −1 (Melanic soils). Although meeting the estimated national soil C sequestration potential (124 Mt C) is unrealistic, improved management practices targeted to those soils with the greatest sequestration potential could contribute significantly to off-setting New Zealand's greenhouse gas emissions. As the first national-scale estimate of SOC sequestration potential that encompasses both Allophanic and non-Allophanic soils, this serves as an informative case study for the international community. This article is protected by copyright. All rights reserved.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Published by Wiley
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  • 3
    Publication Date: 2017-01-05
    Description: COSMIC, the Catalogue of Somatic Mutations in Cancer ( http://cancer.sanger.ac.uk ) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers. Molecular profiling of large tumour numbers has also allowed the annotation of more than 13 million non-coding mutations, 18 029 gene fusions, 187 429 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 abnormal expression variants and 7 879 142 differentially methylated CpG dinucleotides. COSMIC now details the genetics of drug resistance, novel somatic gene mutations which allow a tumour to evade therapeutic cancer drugs. Focusing initially on highly characterized drugs and genes, COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours. All information from the COSMIC database is available freely on the COSMIC website.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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