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

On being the right size: heart design, mitochondrial efficiency and lifespan potential

1. From the smallest shrew or bumble-bee bat to the largest blue whale, heart size varies by over seven orders of magnitude (from 12 mg to 600 kg). This study reviews the scaling relationships between heart design, cellular bioenergetics and mitochondrial efficiencies in mammals of different body sizes.\ud \ud 2. The [31P]-nuclear magnetic resonance-derived [phosphocreatine]/[ATP] ratio in hearts of smaller mammals is significantly higher (2.7 ± 0.3 for mouse; n = 22) than in larger mammals (1.6 ± 0.3 for humans; n = 13).\ud \ud 3. The inverse of the free myocardial cytosolic [ADP] concentration and the cytosolic phosphorylation ratio ([ATP]/[ADP][Pi]) scales with heart size and with absolute mitochondrial and myofibrillar volumes, close to a quarter-power (from −0.22 to −0.28; r = 0.99).\ud \ud 4. Assuming a similar mitochondrial P/O ratio and the same maximal amount of work required to convert 1 mol NADH to 0.5 mol O2 (i.e. 212.25 kJ/mol), the higher [ATP]/[ADP][Pi] ratios or cellular driving forces (ΔG'ATP) in hearts of smaller mammals imply greater mitochondrial efficiencies in coupling ATP production to electron transport as body size decreases. For a P/O ratio of 2.5, the mitochondrial efficiency in the heart of a shrew, mouse, human and whale is 84, 82, 71 and 65%, respectively.\ud \ud 5. Higher cytosolic ATP]/[ADP][Pi] ratios and ΔG'ATP values imply that the hearts of smaller mammals operate further from equilibrium than hearts of larger mammals.\ud \ud 6. As a consequence of scaling relationships, a number of remarkable invariants emerge when comparing heart function from the smallest shrew to the largest whale; the total volume of blood pumped by each heart in a lifetime is approximately 200 million L/kg heart and the total number of heart beats is approximately 1.1 billion per lifetime.\ud \ud 7. Similarly, the metabolic potential (total O2 consumed during adult lifespan per g bodyweight) for a 2 g shrew or a 100 000 kg blue whale is approximately 38 L O2 consumed or 8.5 mol ATP/g body mass per lifetime.\ud \ud 8. The importance of quarter-power scaling relationships linking structural, metabolic and bioenergetic design to the natural ageing process and maximum lifespan potential is discussed