• Login
    View Item 
    •   Home
    • Theses and Dissertations
    • Theses
    • View Item
    •   Home
    • Theses and Dissertations
    • Theses
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of KAUSTCommunitiesIssue DateSubmit DateThis CollectionIssue DateSubmit Date

    My Account

    Login

    Quick Links

    Open Access PolicyORCID LibguidePlumX LibguideSubmit an Item

    Statistics

    Display statistics

    Visualization and Simulation of Variants in Personal Genomes With an Application to Premarital Testing (VSIM)

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Thumbnail
    Name:
    Azza Althagafi_Final Thesis.pdf
    Size:
    1.974Mb
    Format:
    PDF
    Download
    Type
    Thesis
    Authors
    Althagafi, Azza Th. cc
    Advisors
    Hoehndorf, Robert cc
    Committee members
    Moshkov, Mikhail cc
    Gojobori, Takashi cc
    Program
    Computer Science
    KAUST Department
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Date
    2018-11-28
    Embargo End Date
    2019-11-28
    Permanent link to this record
    http://hdl.handle.net/10754/630088
    
    Metadata
    Show full item record
    Access Restrictions
    At the time of archiving, the student author of this thesis opted to temporarily restrict access to it. The full text of this thesis became available to the public after the expiration of the embargo on 2019-11-28.
    Abstract
    Interpretation and simulation of the large-scale genomics data are very challenging, and currently, many web tools have been developed to analyze genomic variation which supports automated visualization of a variety of high throughput genomics data. We have developed VSIM an automated and easy to use web application for interpretation and visualization of a variety of genomics data, it identifies the candidate diseases variants by referencing to four databases Clinvar, GWAS, DIDA, and PharmGKB, and predicted the pathogenic variants. Moreover, it investigates the attitude towards premarital genetic screening by simulating a population of children and analyze the diseases they might be carrying, based on the genetic factors of their parents taking into consideration the recombination hotspots. VSIM supports output formats based on Ideograms that are easy to interpret and understand, which makes it a biologist-friendly powerful tool for data visualization, and interpretation of personal genomic data. Our results show that VSIM can efficiently identify the causative variants by referencing well-known databases for variants in whole genomes associated with different kind of diseases. Moreover, it can be used for premarital genetic screening by simulating a population of offspring and analyze the disorders they might be carrying. The output format provides a better understanding of such large genomics data. VSIM thus helps biologists and marriage counsellor to visualize a variety of genomic variants associated with diseases seamlessly.
    Citation
    Althagafi, A. T. (2018). Visualization and Simulation of Variants in Personal Genomes With an Application to Premarital Testing (VSIM). KAUST Research Repository. https://doi.org/10.25781/KAUST-5O534
    DOI
    10.25781/KAUST-5O534
    ae974a485f413a2113503eed53cd6c53
    10.25781/KAUST-5O534
    Scopus Count
    Collections
    Theses; Computer Science Program; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

    entitlement

     
    DSpace software copyright © 2002-2021  DuraSpace
    Quick Guide | Contact Us | Send Feedback
    Open Repository is a service hosted by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. For anonymous users the allowed maximum amount is 50 search results.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.