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dc.contributor.advisorHoehndorf, Robert
dc.contributor.authorAlthagafi, Azza Th.
dc.date.accessioned2018-11-28T10:41:50Z
dc.date.available2019-11-28T00:00:00Z
dc.date.issued2018-11-28
dc.identifier.citationAlthagafi, 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
dc.identifier.doi10.25781/KAUST-5O534
dc.identifier.urihttp://hdl.handle.net/10754/630088
dc.description.abstractInterpretation 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.
dc.language.isoen
dc.subjectsimulation
dc.subjectvisualization
dc.subjectpremarital
dc.subjectconsanguinity
dc.subjectvariant interpretation
dc.subjectgenetic testing
dc.titleVisualization and Simulation of Variants in Personal Genomes With an Application to Premarital Testing (VSIM)
dc.typeThesis
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.rights.embargodate2019-11-28
thesis.degree.grantorKing Abdullah University of Science and Technology
dc.contributor.committeememberMoshkov, Mikhail
dc.contributor.committeememberGojobori, Takashi
thesis.degree.disciplineComputer Science
thesis.degree.nameMaster of Science
dc.rights.accessrightsAt 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.
refterms.dateFOA2018-11-28T10:43:21Z


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