Phenopolis

An Open Platform for Harmonization & Analysis of Sequencing & Phenotype Data.


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About Phenopolis

Phenopolis is an open platform for harmonization and analysis of sequencing and phenotype data. The Phenopolis code is available at github. Funding is currently provided mainly by RP Fighting Blindness, NIHR (UCL-Moorfields Eyes Hospital Biomedical Research Center) and in part by the UK Medical Research Council and the British Heart Foundation.

The data set provided on this website spans 6053 sequenced individuals. All of the raw data from these projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects.

Behind Phenopolis is a coalition of clinicians, geneticists, bioinformaticians and software engineers seeking to aggregate and harmonize sequencing and phenotype data using the Human Phenotype Ontology.

The Team behind Phenopolis

  • Dr. Nikolas Pontikos
    school UCL Genetics Institute; school Institute of Ophthalmology, UCL; school  Moorfields Eye Hospital, London

    I started the development of Phenopolis.

  • Dr. Jing Yu
    school Nuffield Department of Clinical Neurosciences, University of Oxford school John Radcliffe Hospital, Oxford

    I helped construct the website, and developed pubmedBatch, Phenogenon and several other analyses / visualisations in Phenopolis.

  • Dr. Cian Murphy
    school UCL Genetics Institute

    I developed gene burden tests and run the CNV pipeline (data to be integrated).

  • Daniel Greene
    school Department of Haematology, University of Cambridge; school Medical Research Council Biostatistics Unit, Cambridge

    I helped integrate the SimReg method for discovering genotype-phenotype associations into phenopolis. SimReg evaluates the evidence of association between ontologically encoded phenotypes and rare alleles in given genes. Where there is strong evidence of association, SimReg also estimates a characteristic phenotype for the disease caused by pathogenic variants.

  • Ismail Moghul
    school UCL Cancer Institute

    I worked on the front-end aspect of Phenopolis with a particular focus on improving the user interphase and user experience as well as the general performance of the web application.

  • Dr. Lucy Withington
    school RP Fighting Blindness

    I added the unit test and continuous integration framework and reviewed the security and usability of the website.

  • Dr. Tom Vulliamy
    school Blizard Institute, Queen Mary University of London

    I have been sequencing patients who have a bone marrow failure syndrome that is clinically and genetically heterogeneous.
    We have been trying to identify the genes responsible. Although we have had some success, a significant proportion remain uncharacterised, and we are interesting in novel analysis approaches using the Human Phenotype Ontology.

  • Dr. Fiona Blanco-Kelly
    school Institute of Ophthalmology, UCL; school  Moorfields Eye Hospital, London

    I entered and curated a large number of phenotypes encoded using the Human Phenotype Ontology

  • Baron Koylass
    school UCL Genetics Institute

    I am an MSc student of the Genetics of Human Disease program at University College London, doing my Masters project on Phenopolis.

  • Sajid Mughal
    school UCL Genetics Institute

    I am a software developer developing graph databases for Phenopolis. My project page is here.

The Pitch

Rare disease diagnostic research labs and large initiatives such as Genomics England are generating growing amounts of next generation sequencing data and standardised clinical phenotypes encoded with the Human Phenotype Ontology (HPO).

There is a clear need for a free, easy and effective method of analysing and sharing this wealth of information between clinicians and researchers.

With this goal in mind, we have developed, Phenopolis, an open-source research and diagnosis tool. While there are already several commercial tools that provide filtering and prioritisation of genetic variants (e.g Congenica, Saphetor, Omicia) in patient, there are currently only two other open-source alternatives (Gemini and Seqr), and we are not aware of any tools which supports the type of HPO analysis our platform supports.

Our software unifies existing HPO analysis methods (Exomiser, SimReg) but also our own novel analysis and visualisation methods (PubmedScore, Phenogenon), through an easily extensible interface.

Phenopolis supports three visualisations of the data depending on the research question:

Our software is being actively used by UK universities, UCL, Queen Mary, Leeds, Oxford and Manchester, and has already been referenced in “The Human Phenotype Ontology 2017” update published in the Nucleic Acid Research 2016 (doi:10.1093/nar/gkw1039).

The team behind Phenopolis is a unique combination of software developers, PhD students, postdoctoral bioinformaticians, geneticists and clinicians, all dedicated to free software and data sharing, and has managed, in the space of a year with no project funding to make significant progress.

Seed funding would allow us to purchase the hardware to make our website reliable, add functionality and scale to provide a free service to anyone who wants to have their data analysed. After the funding period, Phenopolis will be connected to the Global Alliance for Genomics and Health network (which includes large patient database such as DECIPHER, PhenomeCentral) and could be used by initiatives such as Genomics England.

Our mission is to guarantee that anyone around the world will be able to use our platform for free to address important research and clinical questions . We think that Phenopolis is promoting an extremely important message of openness and data sharing to solve human disease.