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

Forest Decline after a 15-Year “Perfect Storm” of Invasion by Hemlock Woolly Adelgid, Drought, and Hurricanes

Invasions by introduced pests can interact with other disturbances to alter forests and their functions, particularly when a dominant tree species declines. To identify changes after invasion by the insect hemlock woolly adelgid (Adelges tsugae; HWA), coinciding with severe droughts and hurricanes, this study compared tree species composition of eastern hemlock (Tsuga canadensis) forests on 11 plots before (2001) and 15 years after (2016) invasion in the southern Appalachian Mountains, USA. Losses of hemlock trees after HWA invasion were among the highest reported, with a 90% decline in density, 86% decline in basal area, and 100% mortality for individuals ≥ 60 cm in diameter. In contrast to predictions of theoretical models, deciduous tree density declined after HWA invasion, while basal area changed little, at least during the initial 15 years after invasion. Overall, forest density declined by 58%, basal area by 25%, and tree species richness by 8%. Factors additional to HWA likely exacerbating forest decline included: droughts before (1999–2001) and after HWA invasion (2006–2008); tree uprooting from hurricane-stimulated winds in 2004; pest-related declines of deciduous tree species otherwise likely benefitting from hemlock’s demise; death of deciduous trees when large hemlocks fell; and competition from aggressive understory plants including doghobble (Leucothoe fontanesiana), rosebay rhododendron (Rhododendron maximum), and Rubus spp. Models of forest change and ecosystem function should not assume that deciduous trees always increase during the first decades after HWA invasion