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

Association of Aberrant Posterior Vitreous Detachment and Pathologic Tractional Forces With Myopic Macular Degeneration.

PURPOSE: The purpose of this study was to assess whether the tractional elements of pathologic myopia (PM; e.g. myopic traction maculopathy [MTM], posterior staphyloma [PS], and aberrant posterior vitreous detachment [PVD]) are associated with myopic macular degeneration (MMD) independent of age and axial length, among highly myopic (HM) eyes. METHODS: One hundred twenty-nine individuals with 239 HM eyes from the Myopic and Pathologic Eyes in Singapore (MyoPES) cohort underwent ocular biometry, fundus photography, swept-source optical coherence tomography, and ocular B-scan ultrasound. Images were analyzed for PVD grade, and presence of MTM, PS, and MMD. The χ² test was done to determine the difference in prevalence of MMD between eyes with and without PVD, PS, and MTM. Multivariate probit regression analyses were performed to ascertain the relationship between the potential predictors (PVD, PS, and MTM) and outcome variable (MMD), after accounting for possible confounders (e.g. age and axial length). Marginal effects were reported. RESULTS: Controlling for potential confounders, eyes with MTM have a 29.92 percentage point higher likelihood of having MMD (P = 0.003), and eyes with PS have a 25.72 percentage point higher likelihood of having MMD (P = 0.002). The likelihood of MMD increases by 10.61 percentage points per 1 mm increase in axial length (P < 0.001). Subanalysis revealed that eyes with incomplete PVD have a 22.54 percentage point higher likelihood of having MMD than eyes with early PVD (P = 0.04). CONCLUSIONS: Our study demonstrated an association between tractional (MTM, PS, and persistently incomplete PVD) and degenerative elements of PM independent of age and axial length. These data provide further insights into the pathogenesis of MMD

Metal coordination polymer derived mesoporous Co3O4 nanorods with uniform TiO2 coating as advanced anodes for lithium ion batteries

In this work, a one-dimensional Co3O4@TiO2 core-shell electrode material with superior electrochemical performance is fabricated by a convenient and controllable route. The approach involves two main steps: the homogeneous deposition of polydopamine and TiO2 layers in sequence on the cobalt coordination polymer and the thermal decomposition of the polymer matrix. The as-prepared electrode material can achieve excellent electrochemical properties and stability as an anode material for lithium ion batteries, such as a high specific capacity of 1279 mA h g(-1), good cycling stability (around 803 mA h g-1 at a current density of 200 mA g(-1) after 100 cycles), and stable rate performance (around 520 mA h g(-1) at a current density of 1000 mA g(-1)). This dramatic electrochemical performance is mainly attributed to the excellent structural characteristics, which could improve the electrical conductivity and lithium ion mobility, as well as electrolyte permeability and architectural stability during cycling

Multimodal Imaging-Based Phenotyping of a Singaporean Hospital-Based Cohort of High Myopia Patients.

Purpose: To assess the effect of axial length (AL) on the prevalence of pathologic myopia (PM) and associated myopic features in a Singaporean hospital-based cohort of patient with high myopia (HM). Methods: In total, 923 HM eyes from 495 individuals were recruited from the Myopic and Pathologic Eyes in Singapore (MyoPES) cohort and underwent ocular biometry, fundus photography, fundus autofluorescence, and swept-source optical coherence tomography (SS-OCT). Images were analyzed for the presence of myopic macular degeneration (MMD), myopic choroidal neovascularization (mCNV), myopic traction maculopathy (MTM), peripapillary atrophy (PPA), myopic tilted disc, posterior staphyloma (PS), dome-shaped macula (DSM), vitremacular adhesions (VMA), and the epiretinal membrane (ERM). Eyes were stratified into quartiles based on ALs to determine cut-off values to perform comparisons between shorter-length and longer-length groups. A χ2-test was done to determine the difference in the prevalence of pathologies between groups. Results: Overall, mean AL was 29.2 ± 2.2 mm (range 25.0-36.7 mm). Myopic macular degeneration, PPA, myopic tilted disc, and ERM have AL threshold of ≥27.5 mm, whereas MTM has an AL threshold of ≥29.0 mm. We found that there was a significantly higher prevalence of MMD (88.2 vs. 49.4%; p < 0.001), PPA (98.1 vs. 80.1%; p < 0.001), myopic tilted disc (72.7 vs. 50.2%; p < 0.001), and ERM (81.4 vs. 17.3%; p = 0.003) in eyes with AL ≥ 27.5 mm vs. eyes without AL <27.5 mm. Prevalence of MTM (34.7 vs. 32.1%; p < 0.001), mCNV (17.4 vs. 12.1%; p = 0.03), PS (43.4 vs. 34.7%; p = 0.012), DSM (21.3 vs. 13.2%; p = 0.002), and VMA (5.9 vs. 2.6%; p = 0.014) in eyes with AL ≥ 29.0 mm compared with AL < 29.0 mm. Conclusion: Our study describes the overall prevalence of PM and related pathologies among patients with HM in our hospital-based cohort. Longer eyes even among HM eyes had a significantly higher prevalence of PM-associated pathologies studied. This supports the premise that eyes with longer AL, even among HM eyes may be at greater risk of vision-threatening changes and therefore merit regular follow-up