Suchergebnisse

Cancer is the leading cause of premature death (0-69) in Spain and in the vast majority of countries in the European Union. Developing countries are less a ected but numbers are expected to rise over the next few decades as a consequence of population aging and lifestyle changes. Besides the human losses, cancer is responsible for large economic impact on healthcare systems and companies. It will come as no surprise to learn that many pharmaceutical companies and public funding agencies target cancer as their most funded research topic. Cancer is a complex set of diseases that are normally labeled using the tissue and/or cell type from which they originate. Each type is associated with very di erent prognosis and treatments but in most cases, patients would bene t from early detection, diagnosis and treatment since tumors tend to become more aggressive with time. In the United States, breast and colon cancer mortality rates have dropped 40% in the last 25 years in part as a consequence of achieving earlier diagnoses on average. ; El cáncer es la principal causa de muerte prematura (0-69) en España y en la mayoría de países de la Unión Europea. Los países en desarrollo se encuentran menos afectados, pero se espera que sus cifras aumenten en las próximas décadas como consecuencia del envejecimiento de la población y los cambios en el estilo de vida. Además de las pérdidas humanas, el cáncer es responsable de un gran impacto económico en los sistemas de salud y en las empresas. Por lo tanto, no es de sorprender que muchas farmacéuticas y agencias de investigación hayan hecho del cáncer la enfermedad cuya investigación mejor se financia. El cáncer es en realidad un conjunto heterogéneo de enfermedades que normalmente se denominan usando el tejido a partir del cual se originan. El pronóstico varía mucho en función del tipo de cáncer pero en la inmensa mayoría de casos, los pacientes se ven bene ficiados si se logra una detección precoz, ya que esto facilita también un tratamiento y diagnóstico tempranos, anticipándose así a una mayor progresión tumoral. En Estados Unidos, la mortalidad de cáncer de mama y colon ha disminuido en torno a un 40% en los últimos 25 años. Este descenso se ha logrado, entre otras cosas, como consecuencia de un aumento en los diagnósticos tempranos. ; Tesis Univ. Granada. ; Instituto de Salud Carlos III (Ministerio de Economía y Competitividad) [IFI16/00041] ; Consejería de Salud, Junta de Andalucía [EF-0484-2017] ; Instituto de Salud Carlos III (Ministerio de Economía y Competitividad) [MV19/00058] ; Fulbright Program, Predoctoral Research 2020 Call, Bureau of Educational and Cultural Affairs of the U.S. Department of State, United States of America ; [PIE16/00045] Instituto de Salud Carlos III ; [PI-0533-2014] Fundación progreso y Salud /Consejería de Salud, Junta de Andalucía)

This work was supported by European Union [765492]; Spanish Government [AGL2017-88702-C2-2-R] to M.H.; Consejer´ıa de Econom´ıa, Conocimiento, Empresas y Universidad de la Junta de Andaluc´ıa and European Regional Development Funds (ERDF) [SOMM17-6109, UCE-PP2017-3] to J.A.M. and M.H.; Instituto de Salud Carlos III, ERDF funds [PIE16/00045] to J.A.M.; Chair 'Doctors Galera-Requena in cancer stem cell research' (to J.A.M.); Instituto de Salud Carlos III [IFI16/00041] to E.A. Funding for open access charges: Excellence Research Unit "Modelling Nature" (MNat) [SOMM17-6109]. Conflict of interest statement. None declared. ; Although miRNA-seq is extensively used in many different fields, its quality control is frequently restricted to a PhredScore-based filter. Other important quality related aspects like microRNA yield, the fraction of putative degradation products (such as rRNA fragments) or the percentage of adapter-dimers are hard to assess using absolute thresholds. Here we present mirnaQC, a webserver that relies on 34 quality parameters to assist in miRNA-seq quality control. To improve their interpretability, quality attributes are ranked using a reference distribution obtained from over 36 000 publicly availablemiRNA-seq datasets. Accepted input formats include FASTQ and SRA accessions. The results page contains several sections that deal with putative technical artefacts related to library preparation, sequencing, contamination or yield. Different visualisations, including PCA and heatmaps, are available to help users identify underlying issues. Finally, we show the usefulness of this approach by analysing two publicly available datasets and discussing the different quality issues that can be detected using mirnaQC. ; European Union (EU) 765492 ; Spanish Government AGL2017-88702-C2-2-R ; Junta de Andalucia ; European Union (EU) SOMM17-6109 UCE-PP2017-3 ; Instituto de Salud Carlos III, ERDF funds PIE16/00045 ; Instituto de Salud Carlos III IFI16/00041 ; Chair 'Doctors Galera-Requena in cancer stem cell ...

MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different types of neoplastic, cardiovascular and degenerative diseases. However, many of these studies rely on small RNA sequencing experiments that are based on different RNA extraction and processing protocols, rendering results incomparable. We generated liqDB, a database for liquid biopsy small RNA sequencing profiles that provides users with meaningful information to guide their small RNA liquid biopsy research and to overcome technical and conceptual problems. By means of a user-friendly web interface, miRNA expression profiles from 1607 manually annotated samples can be queried and explored at different levels. Result pages include downloadable expression matrices, differential expression analysis, most stably expressed miRNAs, cluster analysis and relevant visualizations by means of boxplots and heatmaps. We anticipate that liqDB will be a useful tool in liquid biopsy research as it provides a consistently annotated large compilation of experiments together with tools for reproducible analysis, comparison and hypothesis generation. ; European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [grant agreement ELBA, 765492 to M.H. and D.K.L.]; Spanish Government [AGL2017-88702-C2-2-R to M.H.]; Instituto de Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.]; Chair 'Doctors Galera-Requena in cancer stem cell research' (to J.A.M.); Ministry of Education of Spain [FPU13/05662 to R.L. and IFI16/00041 to E.A.]. Funding for open access charge: Instituto de Salud Carlos III (FEDER funds) [PIE16/00045].

European Union [765492 to M.H.]; Spanish Government [AGL2017-88702-C2-2-R to M.H.]; Chair 'Doctors Galera-Requena in cancer stem cell research' (to J.A.M.); Tromsoforskningsstiftelse (TFS) [20 SG BF 'MIRevolution' to B.F.]; Stichting Cancer Center Amsterdam [CCA2021-9-77 to C.G]; TKI-Health Holland ['AQrate' project to C.G. and M.P.]. This publication is part of a project that has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 765492. ; The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performsmapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/. ; European Commission 765492 ; Spanish Government ; European Commission AGL2017-88702-C2-2-R ; Chair 'Doctors Galera-Requena in cancer stem cell research' ; Stichting Cancer Center ...

Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well asmicroRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNAseq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency. ; European Union [765492 to M.H.]; Spanish Government [AGL2017-88702-C2-2-R to M.H., J.L.O.]; Instituto de Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.]; Chair 'Doctors Galera-Requena in cancer stem cell research' to JMA and by the Ministry of Education of Spain [FPU13/05662 to R.L., IFI16/00041 to E.A.]; Strategic Research Area (SFO) program of the Swedish Research Council (to V.R.) through Stockholm University (to B.F.). Funding for open access charge: SpanishGovernment [AGL2017-88702-C2-2-R].