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

Ultrasound assisted extraction of lycopene from tomato processing wastes

Tomato paste processing wastes, an important by-product of the paste industry, is rich in potentially health-promoting compounds such as lycopene. In this study, extraction yield of lycopene from tomato paste processing wastes by application of ultrasound assisted extraction (UAE) was compared with conventional organic solvent extraction (COSE) method. BHT (butylated hydroxytoluene) 0.05 % (w/v) added hexane:acetone:ethanol (2:1:1) mixture was used as solvent. Three different solvent solid ratios; 50:1, 35:1 and 20:1, (v/w) were used in both COSE and UAE. COSE experiments were performed at 20 °C, 40 °C and 60 °C for 10, 20, 30 and 40 min. 50, 65 and 90 W of ultrasonic power were applied in UAE for 1, 2, 5, 10, 15, 20 and 30 min. Lycopene contents of the samples were determined by spectrophotometric method. The effects of different factors, including the temperature, solvent solid ratio and ultrasonic power on lycopene yield were investigated. It was determined that the most efficient application for COSE was extracting samples by 50:1 solvent solid ratio at 60 °C for 40 min run, for UAE, 35:1 (v/w) solvent solid ratio, 90 W ultrasonic power for 30 min run. It was showed that UAE of lycopene requires less time, lower temperature and lower solvent than COSE

Techno-economic Assessment Methodology for Ultrasonic Production of Biofuels

Many market introductions fail due to economic reasons and not because of process performance. A techno-economic assessment (TEA) tool can help in making good choices during process development and raise the success rate of market introduction. In this chapter, the advantages of performing a TEA in early development stage of an innovative technology are highlighted. Seeing the current state of ultrasound technology, a TEA can help to steer further research into the most interesting pathway. The chapter, therefore, elaborates on the methodology that can be used to perform such a TEA and on the specific components which should be taken into account when applying a TEA on the ultrasonic production of biofuels and chemicals. Finally, a review is provided on the existing scientific literature concerning the economic performance of ultrasound technology.techno-economic assessment; cost-benefit analysis; mass balance; energy balance; biofuels; ultrasoun