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

Artemia feeds: a review of brine shrimp production in the Mekong Delta, Vietnam

Seasonal Artemia pond production has been practiced for several decades by rural salt producing communities in the Mekong Delta, Vietnam, with more success than elsewhere in the world. In spite of this success, yields have been stagnating for a long time due to suboptimal feeding conditions. As feeding is one of the most important factors affecting Artemia production, the aim of this article was to review the studies that have been done so far on the development and application of appropriate Artemia feeds and feeding protocols in this area. So far, there are three main approaches. Traditionally, phytoplankton blooming is stimulated by the use of fertilizers in so-called fertilization ponds. This green water is supplemented by the use of cheap agriculture waste products and chicken manure, directly applied in Artemia ponds. As this technique, however, often results in suboptimal feeding levels and comes with high nutrient charges in pond effluents, recently a formulated feed has been developed specifically for Artemia pond production which allows further increasing production levels. Finally, also the biofloc technology can be applied in Artemia culture by adding tapioca flour or molasses as carbon source to obtain the ratio C/N >= 10 in order to stimulate biofloc development as feed for Artemia in ponds. The limitations of the above techniques are discussed. It is envisaged that the future success and further expansion of Artemia pond production, also outside Vietnam, will increasingly be determined by a flexible use of a combination of these techniques