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

Crystal structures and magnetic properties of Fe_1.93-xCo_xP_1-ySi_y compounds

In view of the interest that (Fe,Co)2(P,Si) compounds have as potential permanent magnets, their structural and magnetic phase diagrams are explored focusing on establishing the range where the hexagonal Fe2P-type structure is observed. In Fe1.93-xCoxP1-ySiy, the highest Si content prior entering a mixed phase domain is y ≈ 0.5. At high Si content but low Co for Fe substitutions, a structural distortion leading to a body-centered orthorhombic structure occurs. At high Co contents, when the Fe2P unit cell reaches a critical volume of about 102.4 Å3, the samples crystallize in a Co2P-type orthorhombic structure. Within the Fe2P-type structural range, the evolution of the unit-cell volume appears to follow the Vegard's law, but this hides strongly anisotropic changes. Simultaneous Co for Fe and Si for P substitutions increase the range where the hexagonal structure is observed in comparison to ternary Fe2(P,Si) and (Fe,Co)2P. The samples are ferromagnetic, but with Curie temperatures showing an unusual evolution, uncorrelated to the c/a ratio of the lattice parameters. At low Si content, TC increases with Co for Fe substitutions. For y = 0.2, the evolution is not significant, while at high Si content TC systematically decreases with the increase in Co. Large Si and Co substitutions lead to a swift weakening of the magnetocrystalline anisotropy until the easy axis anisotropy turns from the c axis toward the a-b plane. This study guides future investigations by restricting the range where desirable properties for permanent magnetic applications can be expected to 0.1 ≲ x ≲ 0.3 and 0.1 ≲ y ≲ 0.3.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.RST/Fundamental Aspects of Materials and Energ