GenExp: An Interactive Web-Based Genomic DAS Client with Client-Side Data Rendering

Background: The Distributed Annotation System (DAS) offers a standard protocol for sharing and integrating annotations on biological sequences. There are more than 1000 DAS sources available and the number is steadily increasing. Clients are an essential part of the DAS system and integrate data from several independent sources in order to create a useful representation to the user. While web-based DAS clients exist, most of them do not have direct interaction capabilities such as dragging and zooming with the mouse. Results: Here we present GenExp, a web based and fully interactive visual DAS client. GenExp is a genome oriented DAS client capable of creating informative representations of genomic data zooming out from base level to complete chromosomes. It proposes a novel approach to genomic data rendering and uses the latest HTML5 web technologies to create the data representation inside the client browser. Thanks to client-side rendering most position changes do not need a network request to the server and so responses to zooming and panning are almost immediate. In GenExp it is possible to explore the genome intuitively moving it with the mouse just like geographical map applications. Additionally, in GenExp it is possible to have more than one data viewer at the same time and to save the current state of the application to revisit it later on. Conclusions: GenExp is a new interactive web-based client for DAS and addresses some of the short-comings of the existin

Dissemination and visualisation of biological data

With the recent advent of various waves of technological advances, the amount of biological data being generated has exploded. As a consequence of this data deluge, new challenges have emerged in the field of biological data management. In order to maximize the knowledge extracted from the huge amount of biological data produced it is of great importance for the research community that data dissemination and visualisation challenges are tackled. Opening and sharing our data and working collaboratively will benefit the scientific community as a whole and to move towards that end, new developements, tools and techniques are needed. Nowadays, many small research groups are capable of producing important and interesting datasets. The release of those datasets can greatly increase their scientific value. In addition, the development of new data analysis algorithms greatly benefits from the availability of a big corpus of annotated datasets for training and testing purposes, giving new and better algorithms to biomedical sciences in return. None of these would be feasible without large amounts of biological data made freely and publicly available. Dissemination The Distributed Annotation System (DAS) is a protocol designed to publish and integrate annotations on biological entities in a distributed way. DAS is structured as a client-server system where the client retrieves data from one or more servers and to further process and visualise. Nowadays, setting up a DAS server imposes some requirements not met by many research groups. With the aim of removing the hassle of setting up a DAS server, a new software platform has been developed: easyDAS. easyDAS is a hosted platform to automatically create DAS servers. Using a simple web interface the user can upload a data file, describe its contents and a new DAS server will be automatically created and data will be publicly available to DAS clients. Visualisation One of the most broadly used visualization paradigms for genomic data are genomic browsers. A genomic browser is capable of displaying different sets of features positioned relative to a sequence. It is possible to explore the sequence and the features by moving around and zooming in and out. When this project was started, in 2007, all major genome browsers offered quite an static experience. It was possible to browse and explore data, but is was done through a set of buttons to the genome a certain amount of bases to left or right or zooming in and out. From an architectural point of view, all web-based genome browsers were very similar: they all had a relatively thin clien-side part in charge of showing images and big backend servers taking care of everything else. Every change in the display parameters made by the user triggered a request to the server, impacting the perceived responsiveness. We created a new prototype genome browser called GenExp, an interactive web-based browser with canvas based client side data rendering. It offers fluid direct interaction with the genome representation and it's possible to use the mouse drag it and use the mouse wheel to change the zoom level. GenExp offers also some quite unique features, such as its multi-window capabilities that allow a user to create an arbitrary number of independent or linked genome windows and its ability to save and share browsing sessions. GenExp is a DAS client and all data is retrieved from DAS sources. It is possible to add any available DAS data source including all data in Ensembl, UCSC and even the custom ones created with easyDAS. In addition, we developed a javascript DAS client library, jsDAS. jsDAS is a complete DAS client library that will take care of everything DAS related in a javascript application. jsDAS is javascript library agnostic and can be used to add DAS capabilities to any web application. All software developed in this thesis is freely available under an open source license.Les recents millores tecnològiques han portat a una explosió en la quantitat de dades biològiques que es generen i a l'aparició de nous reptes en el camp de la gestió de les dades biològiques. Per a maximitzar el coneixement que podem extreure d'aquestes ingents quantitats de dades cal que solucionem el problemes associats al seu anàlisis, i en particular a la seva disseminació i visualització. La compartició d'aquestes dades de manera lliure i gratuïta pot beneficiar en gran mesura a la comunitat científica i a la societat en general, però per a fer-ho calen noves eines i tècniques. Actualment, molts grups són capaços de generar grans conjunts de dades i la seva publicació en pot incrementar molt el valor científic. A més, la disponibilitat de grans conjunts de dades és necessària per al desenvolupament de nous algorismes d'anàlisis. És important, doncs, que les dades biològiques que es generen siguin accessibles de manera senzilla, estandaritzada i lliure. Disseminació El Sistema d'Anotació Distribuïda (DAS) és un protocol dissenyat per a la publicació i integració d'anotacions sobre entitats biològiques de manera distribuïda. DAS segueix una esquema de client-servidor, on el client obté dades d'un o més servidors per a combinar-les, processar-les o visualitzar-les. Avui dia, però, crear un servidor DAS necessita uns coneixements i infraestructures que van més enllà dels recursos de molts grups de recerca. Per això, hem creat easyDAS, una plataforma per a la creació automàtica de servidors DAS. Amb easyDAS un usuari pot crear un servidor DAS a través d'una senzilla interfície web i amb només alguns clics. Visualització Els navegadors genomics són un dels paradigmes de de visualització de dades genòmiques més usats i permet veure conjunts de dades posicionades al llarg d'una seqüència. Movent-se al llarg d'aquesta seqüència és possibles explorar aquestes dades. Quan aquest projecte va començar, l'any 2007, tots els grans navegadors genomics oferien una interactivitat limitada basada en l'ús de botons. Des d'un punt de vista d'arquitectura tots els navegadors basats en web eren molt semblants: un client senzill encarregat d'ensenyar les imatges i un servidor complex encarregat d'obtenir les dades, processar-les i generar les imatges. Així, cada canvi en els paràmetres de visualització requeria una nova petició al servidor, impactant molt negativament en la velocitat de resposta percebuda. Vam crear un prototip de navegador genòmic anomenat GenExp. És un navegador interactiu basat en web que fa servir canvas per a dibuixar en client i que ofereix la possibilitatd e manipulació directa de la respresentació del genoma. GenExp té a més algunes característiques úniques com la possibilitat de crear multiples finestres de visualització o la possibilitat de guardar i compartir sessions de navegació. A més, com que és un client DAS pot integrar les dades de qualsevol servidor DAS com els d'Ensembl, UCSC o fins i tot aquells creats amb easyDAS. A més, hem desenvolupat jsDAS, la primera llibreria de client DAS completa escrita en javascript. jsDAS es pot integrar en qualsevol aplicació DAS per a dotar-la de la possibilitat d'accedir a dades de servidors DAS. Tot el programari desenvolupat en el marc d'aquesta tesis està lliurement disponible i sota una llicència de codi lliure

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data

Altres ajuts: Plan Estatal de I+D+I 2013-16; Asociación Española Contra en CáncerAbstract. Motivation: Data visualization is a crucial tool for data Exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species. Results: We have developed karyoploteR, an R/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them. Plot creation process is inspired in R base graphics, with a main function creating karyoplots with no data and multiple additional functions, including custom functions written by the end-user, adding data and other graphical elements. This approach allows the creation of highly customizable plots from arbitrary data with complete freedomon data positioning and representation. Availability and implementation: karyoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor http://www.bioconductor.org/pack ages/karyoploteR) and at the examples and tutorial page at https://bernatgel.gitHub.io/karyoploter_ tutorial. Contact: [email protected]

easyDAS: Automatic creation of DAS servers

Background: The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process. Results: Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license. Conclusions: easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community.Postprint (published version

Applying Microsatellite Multiplex PCR Analysis (MMPA) for Determining Allele Copy-Number Status and Percentage of Normal Cells within Tumors

The study of somatic genetic alterations in tumors contributes to the understanding and management of cancer. Genetic alterations, such us copy number or copy neutral changes, generate allelic imbalances (AIs) that can be determined using polymorphic markers. Here we report the development of a simple set of calculations for analyzing microsatellite multiplex PCR data from control-tumor pairs that allows us to obtain accurate information not only regarding the AI status of tumors, but also the percentage of tumor-infiltrating normal cells, the locus copy-number status and the mechanism involved in AI. We validated this new approach by re-analyzing a set of Neurofibromatosis type 1-associated dermal neurofibromas and comparing newly generated data with results obtained for the same tumors in a previous study using MLPA, Paralog Ratio Analysis and SNP-array techniques. Microsatellite multiplex PCR analysis (MMPA) should be particularly useful for analyzing specific regions of the genome containing tumor suppressor genes and also for determining the percentage of infiltrating normal cells within tumors allowing them to be sorted before they are analyzed by more expensive techniques

Lestaurtinib Inhibition of the JAK/STAT Signaling Pathway in Hodgkin Lymphoma Inhibits Proliferation and Induces Apoptosis

Standard cytotoxic chemotherapy for Hodgkin Lymphoma (HL) has changed little in 30 years; the treatment for patients with relapsed or refractory disease remains challenging and novel agents are under development. JAK/STAT constitutive activation plays an important role in the pathogenesis of HL. Lestaurtinib is an orally bioavailable multikinase inhibitor that has recently been shown to inhibit JAK2 in myeloproliferative disorders. The potential role of Lestaurtinib in HL therapy is unknown. We have analyzed the effect of Lestaurtinib treatment in five HL cell lines from refractory patients, L-428, L-1236, L-540, HDML-2 and HD-MY-Z. At 48 h, a dose-dependent cell growth inhibition (23%–66% at 300 nM) and apoptotic increment (10%–64% at 300 nM) were observed. Moreover, Lestaurtinib inhibited JAK2, STAT5 and STAT3 phosphorylation and reduced the mRNA expression of its downstream antiapoptotic target Bcl-xL. In addition, we have analyzed the effect of Lestaurtinib treatment in lymph nodes from four classic HL patients. We observed a decrease in cell viability at 24 hours of treatment in three patients (mean decrease of 27% at 300 nM). Our findings provide, for the first time, a molecular rationale for testing JAK2 inhibitors, specifically Lestaurtinib, in HL patients

Unbalancing cAMP and Ras/MAPK pathways as a therapeutic strategy for cutaneous neurofibromas

Cutaneous neurofibromas (cNFs) are benign Schwann cell (SC) tumors arising from subepidermal glia. Individuals with neurofibromatosis type 1 (NF1) may develop thousands of cNFs, which greatly affect their quality of life. cNF growth is driven by the proliferation of NF1-/- SCs and their interaction with the NF1+/- microenvironment. We analyzed the crosstalk between human cNF-derived SCs and fibroblasts (FBs), identifying an expression signature specific to the SC-FB interaction. We validated the secretion of proteins involved in immune cell migration, suggesting a role of SC-FB crosstalk in immune cell recruitment. The signature also captured components of developmental signaling pathways, including the cAMP elevator G protein-coupled receptor 68 (GPR68). Activation of Gpr68 by ogerin in combination with the MEK inhibitor (MEKi) selumetinib reduced viability and induced differentiation and death of human cNF-derived primary SCs, a result corroborated using an induced pluripotent stem cell-derived 3D neurofibromasphere model. Similar results were obtained using other Gpr68 activators or cAMP analogs/adenylyl cyclase activators in combination with selumetinib. Interestingly, whereas primary SC cultures restarted their proliferation after treatment with selumetinib alone was stopped, the combination of ogerinselumetinib elicited a permanent halt on SC expansion that persisted after drug removal. These results indicate that unbalancing the Ras and cAMP pathways by combining MEKi and cAMP elevators could be used as a potential treatment for cNFs

Dasty3, a WEB framework for DAS

Motivation: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification

CNVfilteR: an R/bioconductor package to identify false positives produced by germline NGS CNV detection tools.

Germline copy-number variants (CNVs) are relevant mutations for multiple genetics fields, such as the study of hereditary diseases. However, available benchmarks show that all next-generation sequencing (NGS) CNV calling tools produce false positives. We developed CNVfilteR, an R package that uses the single nucleotide variant calls usually obtained in germline NGS pipelines to identify those false positives. The package can detect both false deletions and false duplications. We evaluated CNVfilteR performance on callsets generated by 13 CNV calling tools on 3 whole-genome sequencing and 541 panel samples, showing a decrease of up to 44.8% in false positives and consistent F1-score increase. Using CNVfilteR to detect false-positive calls can improve the overall performance of existing CNV calling pipelines. Availability: CNVfilteR is released under Artistic-2.0 License. Source code and documentation are freely available at Bioconductor (http://www.bioconductor.org/packages/CNVfilteR). Supplementary information: Supplementary data are available at Bioinformatics online