Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). 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 promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Isotopic evidence for dietary niche overlap between barking deer and four-horned antelope in Nepal

BACKGROUND: Morphologically similar sympatric species may have a high degree of niche overlap. Barking deer Muntiacus vaginalis and four-horned antelope Tetracerus quadricornis are solitary ungulates of the Indian sub-continent. Limited information is available regarding their trophic ecology, particularly of the endemic four-horned antelope. We present stable carbon (δ(13)C), nitrogen (δ(15)N), and sulphur (δ(34)S) isotopic values, and nitrogen content (%N) of faeces from barking deer and four-horned antelope living in lowland Nepal to assess trophic niche differentiation of these herbivores along the browser-grazer continuum. We also describe trophic differences between those two species in ecological niches and seasonal effects on their diets. RESULTS: We found that the barking deer and four-horned antelope consumed C(3) plant sources exclusively. The niche partitioning in their diet was reflected by δ(34)S values. Some seasonal effects observed were: δ(13)C and δ(15)N were significantly lower in the dry season diet of four-horned antelope than that of barking deer, while δ(34)S values were significantly higher in the winter diet; monsoon diet was similar for both species. Faecal N levels for barking deer and four-horned antelope were similar throughout all the seasons, indicating that both species adapted their feeding behaviour so as to maximize protein intake, in accordance with season and environment. CONCLUSIONS: Barking deer and four-horned antelope both are browsers; their dietary sources overlapped during monsoon but differed during the dry season. Conservation actions focused on resource management during the dry season to reduce food scarcity and competition over limited resources is likely to be the most effective. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40709-015-0029-0) contains supplementary material, which is available to authorized users

Electrospinning of hydrogels for biomedical applications

The field of biomedical applications for hydrogels requires the development of nanostructures with specific controlled diameter and mechanical properties. Nanofibers are ideally candidates for these advanced requirements, and one of the easiest techniques that can produce one-dimensional nanostructured materials in fibrous form is the electrospinning. This technique provides extremely thin fibres with controlled diameter, highly porous microstructure with interconnected pores; extremely versatile allowing the use of various polymers for tailoring various applications requirements and it is a simple cost-effective method on preparation of scaffolds. In this section, we will discuss recent and specific applications with a focus on their mechanisms. As such, we conclude this section with a discussion on perspectives and future possibilities on this field.ye

Global variation in anastomosis and end colostomy formation following left-sided colorectal resection

Background End colostomy rates following colorectal resection vary across institutions in high-income settings, being influenced by patient, disease, surgeon and system factors. This study aimed to assess global variation in end colostomy rates after left-sided colorectal resection. Methods This study comprised an analysis of GlobalSurg-1 and -2 international, prospective, observational cohort studies (2014, 2016), including consecutive adult patients undergoing elective or emergency left-sided colorectal resection within discrete 2-week windows. Countries were grouped into high-, middle- and low-income tertiles according to the United Nations Human Development Index (HDI). Factors associated with colostomy formation versus primary anastomosis were explored using a multilevel, multivariable logistic regression model. Results In total, 1635 patients from 242 hospitals in 57 countries undergoing left-sided colorectal resection were included: 113 (6·9 per cent) from low-HDI, 254 (15·5 per cent) from middle-HDI and 1268 (77·6 per cent) from high-HDI countries. There was a higher proportion of patients with perforated disease (57·5, 40·9 and 35·4 per cent; P < 0·001) and subsequent use of end colostomy (52·2, 24·8 and 18·9 per cent; P < 0·001) in low- compared with middle- and high-HDI settings. The association with colostomy use in low-HDI settings persisted (odds ratio (OR) 3·20, 95 per cent c.i. 1·35 to 7·57; P = 0·008) after risk adjustment for malignant disease (OR 2·34, 1·65 to 3·32; P < 0·001), emergency surgery (OR 4·08, 2·73 to 6·10; P < 0·001), time to operation at least 48 h (OR 1·99, 1·28 to 3·09; P = 0·002) and disease perforation (OR 4·00, 2·81 to 5·69; P < 0·001). Conclusion Global differences existed in the proportion of patients receiving end stomas after left-sided colorectal resection based on income, which went beyond case mix alone