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

Modelling energy utilization for laying type Pullets

Three trials were carried out to determine energy metabolized (EM) requirement model for starting and growing pullets from different strains, at five ambient temperatures and different percentage feather coverage. In Trial I, metabolizable energy requirements for maintenance (MEm) and efficiency of energy utilization were estimated using 64 birds of two different strains, Hy-Line W36 (HLW36) and Hy-Line Semi-heavy (HLSH), from 9 to 13 weeks of age. The effects of ambient temperature (12, 18, 24, 30 and 36ºC) and percentage feather coverage (0, 50 and 100%) on MEm were assessed in the second trial, using 48 birds per temperature per strain (HLSH and HLW36) from 9 to 13 weeks of age. Trial III evaluated ME requirements for weight gain (MEg) using 1,200 birds from two light strains (HLW36 and Hisex Light, HL) and two semi-heavy strains (HLSH and Hisex Semi-heavy, HSH) reared until 18 weeks of age. According to the prediction models, MEm changed as a function of temperature and feather coverage, whereas MEg changed as a function of age and bird strain. Thus, two models were developed for birds aged 1 to 6 weeks, one model for the light strain and one for the semi-heavy strain. Energy requirements (ER) were different among strains from 7 to 12 weeks, and therefore 4 models were elaborated. From 13 to 18 weeks, one single model was produced for semi-heavy birds, since ER between semi-heavy strains were not different, whereas two different models were elaborated for the light layers. MEg of light birds was higher than MEg of semi-heavy birds, independent of age

Plant extracts used as growth promoters in broilers

Two experiments were carried out to assess the efficacy of plant extracts as alternatives for antimicrobial growth promoters in broiler diets. The performance experiment included 1,200 male broilers raised from 1 to 42 days of age. The metabolism experiment used 96 male broilers in the grower phase housed in metabolic cages for total excreta collection. At the end of the metabolism experiment, 24 birds were sacrificed to assess organ morphometrics. In both experiments, the following treatments were applied: control diet (CD); CD + 10 ppm avilamycin; CD + 1000 ppm oregano extract; CD + 1000 ppm clove extract; CD + 1000 ppm cinnamon extract; and CD + 1000 ppm red pepper extract. The microencapsulated extracts contained 20% of essential oil. No significant differences (P>0.05) in the studied performance parameters were observed among treatments. The dietary supplementation of the extracts did not influence (P>0.05) nitrogen-corrected apparent metabolizable energy values. In general, organ morphometrics was not affected by the experimental treatments, but birds fed the control diet had higher liver relative weight (P<0.05) as compared to those fed the diet containing red pepper extract, which presented the lowest liver relative weight. These results showed that there was no effect of the tested plant extracts on live performance or in organ morphometrics