Suchergebnisse

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 ...

We would like to thank Stephanie Davis for her language editing assistance. The investigators also wish to thank the patients for kindly agreeing to donate samples to this study. We thank all the physicians who collaborated by providing clinical information. Graphical Abstract, Figs 1A, 8A and Fig. S1 were created with Biorender.com. This project has received funding from a European Union's Horizon 2020 research and innovation program under the Marie SklodowskaCurie grant agreement ELBA No 765492. ; Although many studies highlight the implication of circular RNAs (circRNAs) in carcinogenesis and tumor progression, their potential as cancer biomarkers has not yet been fully explored in the clinic due to the limitations of current quantification methods. Here, we report the use of the nCounter platform as a valid technology for the analysis of circRNA expression patterns in non-small cell lung cancer (NSCLC) specimens. Under this context, our custom-made circRNA panel was able to detect circRNA expression both in NSCLC cells and formalin-fixed paraffinembedded (FFPE) tissues. CircFUT8 was overexpressed in NSCLC, contrasting with circEPB41L2, circBNC2, and circSOX13 downregulation even at the early stages of the disease. Machine learning (ML) approaches from different paradigms allowed discrimination of NSCLC from nontumor controls (NTCs) with an 8-circRNA signature. An additional 4-circRNA signature was able to classify early-stage NSCLC samples from NTC, reaching a maximum area under the ROC curve (AUC) of 0.981. Our results not only present two circRNA signatures with diagnosis potential but also introduce nCounter processing following ML as a feasible protocol for the study and development of circRNA signatures for NSCLC. ; European Commission 765492

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].