RESUMEN
Gliomas are the most frequent malignant and aggressive tumors in the central nervous system. Early and effective diagnosis of glioma using diagnostic biomarkers can prolong patients' lives and aid in the development of new personalized treatments. Therefore, a thorough and comprehensive understanding of the diagnostic biomarkers in gliomas is of great significance. To this end, we developed the integrated and web-based database GlioMarker (http://gliomarker.prophetdb.org/), the first comprehensive database for knowledge exploration of glioma diagnostic biomarkers. In GlioMarker, accurate information on 406 glioma diagnostic biomarkers from 1559 publications was manually extracted, including biomarker descriptions, clinical information, associated literature, experimental records, associated diseases, statistical indicators, etc. Importantly, we integrated many external resources to provide clinicians and researchers with the capability to further explore knowledge on these diagnostic biomarkers based on three aspects. (1) Obtain more ontology annotations of the biomarker. (2) Identify the relationship between any two or more components of diseases, drugs, genes, and variants to explore the knowledge related to precision medicine. (3) Explore the clinical application value of a specific diagnostic biomarker through online analysis of genomic and expression data from glioma cohort studies. GlioMarker provides a powerful, practical, and user-friendly web-based tool that may serve as a specialized platform for clinicians and researchers by providing rapid and comprehensive knowledge of glioma diagnostic biomarkers to subsequently facilitates high-quality research and applications.
RESUMEN
Interactive visualization is an effective way to promote the reproducibility of results presented in biomedical publications and to facilitate additional exploration of the reported data. However, there is a lack of convenient tools that balance reproducibility with ease of use. To address this problem, we develop BioVisReport, a lightweight solution for the rapid generation of an interactive website based on a user-defined Markdown file, which acts as a text markup language without requiring users to master complex syntax and allows them to preview the results in real-time. Interactive websites generated by the tool can help readers conveniently reproduce research findings and perform further in-depth analyses beyond those reported in the original peer-reviewed publications. Currently, BioVisReport offers 17 basic types of plots for visualizing published data. In addition, the extensibility of BioVisReport supports flexible integration of user-developed Python plugins with multiple programming languages. BioVisReport is freely available at https://biovis.report/.
RESUMEN
Adenocarcinoma in situ and minimally invasive adenocarcinoma are the pre-invasive forms of lung adenocarcinoma. The genomic and immune profiles of these lesions are poorly understood. Here we report exome and transcriptome sequencing of 98 lung adenocarcinoma precursor lesions and 99 invasive adenocarcinomas. We have identified EGFR, RBM10, BRAF, ERBB2, TP53, KRAS, MAP2K1 and MET as significantly mutated genes in the pre/minimally invasive group. Classes of genome alterations that increase in frequency during the progression to malignancy are revealed. These include mutations in TP53, arm-level copy number alterations, and HLA loss of heterozygosity. Immune infiltration is correlated with copy number alterations of chromosome arm 6p, suggesting a link between arm-level events and the tumor immune environment.
Asunto(s)
Adenocarcinoma in Situ/genética , Adenocarcinoma del Pulmón/genética , Neoplasias Pulmonares/genética , Adenocarcinoma in Situ/inmunología , Adenocarcinoma in Situ/patología , Adenocarcinoma del Pulmón/inmunología , Adenocarcinoma del Pulmón/patología , Adulto , Anciano , Anciano de 80 o más Años , Variaciones en el Número de Copia de ADN , Receptores ErbB/genética , Femenino , Perfilación de la Expresión Génica , Antígenos HLA/genética , Antígenos HLA/inmunología , Humanos , Pérdida de Heterocigocidad , Neoplasias Pulmonares/inmunología , Neoplasias Pulmonares/patología , MAP Quinasa Quinasa 1/genética , Masculino , Persona de Mediana Edad , Mutación , Invasividad Neoplásica , Proteínas Proto-Oncogénicas B-raf/genética , Proteínas Proto-Oncogénicas c-met/genética , Proteínas Proto-Oncogénicas p21(ras)/genética , Proteínas de Unión al ARN/genética , Receptor ErbB-2/genética , Receptores de Antígenos de Linfocitos B/genética , Receptores de Antígenos de Linfocitos T/genética , Proteína p53 Supresora de Tumor/genética , Secuenciación del ExomaRESUMEN
Elucidating the mechanisms underlying the genetic divergence between closely related species is crucial to understanding the origin and evolution of biodiversity. The genus Aquilegia L. has undergone rapid adaptive radiation, generating about 70 well-recognized species that are specialized to distinct habitats and pollinators. In this study, to address the underlying evolutionary mechanisms that drive the genetic divergence, we analyzed the whole genomes of two ecologically isolated Aquilegia species, A. oxysepala and A. japonica as well as their putative hybrid. Our comparative genomic analyses reveal that while the two species diverged only recently and experienced recurrent gene flow, a high level of genetic divergence is observed in their nuclear genomes. In particular, candidate genomic regions that show signature of selection differ dramatically between the two species. Given that the splitting time of the two species is broadly matched with the decrease in effective population sizes, we propose that allopatric isolation together with natural selection have preceded the interspecific gene flow in the process of speciation. The observed high genetic divergence is likely an outcome of combined effects of natural selection, genetic drift and divergent sorting of ancestral polymorphisms. Our study provides a genome-wide view of how genetic divergence has evolved between closely related species.