Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Has Technological Progress Contributed to the Bias of Green Output in China’s Marine Economy?

At present, the destruction of the marine ecological environment and the imbalance of economic structure have put forward urgent requirements for the green development of the marine economy. Based on the input and output data of China’s coastal provinces from 2006 to 2018, the RDM (range directional model) direction distance function was used to measure the output bias technology progress (OBTC) index of each region, and its influence on China’s marine economy green total factor productivity (GTFP) was judged accordingly. Furthermore, the rationality of the current OBTC index was studied. The results show that there is obvious output-biased technological progress in China’s marine economy, and it has led to the improvement of the GTFP. Although most coastal areas still tend to pursue the improvement of the total output value of the marine economy at the expense of environmental damage, the green bias of China’s marine economy has improved significantly since 2015, driven by relevant marine environmental protection policies. From the perspective of different areas, the imbalance of regional development in the process of China’s marine economic development is significant. The green bias of the marine economy is highest in the East China Sea area and lowest in the Bohai rim area. However, the coordination between the development of the green marine economy and environmental protection in the South China Sea area needs to be improved

How does innovation spirit affect R&D investment and innovation performance? The moderating role of business environment

As a vital component of entrepreneurship, innovation spirit is significant for innovation performance. Utilizing the 2015 China Micro and Small Enterprise Survey dataset, we used the Probit and Tobit micro-econometric models to study the relationship between the innovation spirit, research and development (R&D) investment, and innovation performance of micro and small enterprises (MSEs). Our research results show that the innovation spirit of MSEs has a significant promotional effect on innovation performance, and R&D investment is an important internal transmission mechanism for innovation spirit to affect innovation performance. We found that the business environment significantly moderates the impact of innovation spirit on R&D investment and innovation performance. Optimizing the business environment will suppress the impact of innovation spirit on R&D investment and enhance the promotion of innovation spirit on innovation performance. Our results have implications for policymakers about the cultivation of the innovation spirit of MSEs, the optimization of the business environment, and the improvement of the innovation ability of enterprises and the innovation vitality of the market

Enhanced Crystalline Phase Purity of CH₃NH₃PbI_3–<i>x</i>Cl<i>_x</i> Film for High-Efficiency Hysteresis-Free Perovskite Solar Cells

Despite rapid successful developments toward promising perovskite solar cells (PSCs) efficiency, they often suffer significant hysteresis effects. Using synchrotron-based grazing incidence X-ray diffraction (GIXRD) with different probing depths by varying the incident angle, we found that the perovskite films consist of dual phases with a parent phase dominant in the interior and a child phase with a smaller (110) interplanar space (<i>d</i>₍₁₁₀₎) after rapid thermal annealing (RTA), which is a widely used post treatment to improve the crystallization of solution-processed perovskite films for high-performance planar PSCs. In particular, the child phase composition gradually increases with decreasing depth till it becomes the majority on the surface, which might be one of the key factors related to hysteresis in fabricated PSCs. We further improve the crystalline phase purity of the solution-processed CH₃NH₃PbI_3–<i>x</i>Cl<i>_x</i> perovskite film (referred as <i>g</i>-perovskite) by using a facile gradient thermal annealing (GTA), which shows a uniformly distributed phase structure in pinhole-free morphology with less undercoordinated Pb and I ions determined by synchrotron-based GIXRD, grazing incidence small-angle X-ray scattering, scanning electron microscopy, and X-ray photoelectron spectroscopy. Regardless of device structures (conventional and inverted types), the planar heterojunction PSCs employing CH₃NH₃PbI_3–<i>x</i>Cl<i>_x</i> <i>g</i>-perovskite films exhibit negligible hysteresis with a champion power conversion efficiency of 17.04% for TiO₂-based conventional planar PSCs and 14.83% for poly­(3,4-ethylenedioxythiophene:poly­(styrenesulfonate) (PEDOT:PSS)-based inverted planar PSCs. Our results indicate that the crystalline phase purity in CH₃NH₃PbI_3–<i>x</i>Cl<i>_x</i> perovskite film, especially in the surface region, plays a crucial role in determining the hysteresis effect and device performance

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts