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SNPs and Indels Analysis in Human Genome using Computer Simulation and Sequencing Data

Chakrabortty, Sharmistha
http://orcid.org/0000-0003-1139-6189
http://rave.ohiolink.edu/etdc/view?acc_num=mco1501726874739045

Abstract Details

2017, Master of Science in Biomedical Sciences (MSBS), University of Toledo, Biomedical Sciences (Bioinformatics and Proteomics/Genomics).
Genetic variations are the heritable changes in DNA caused by mutation and can be present in both coding and non-coding region of the DNA. They provide great resources for the evolution of an organism in response to environmental and biological changes. Analysis of these variants (such as Single Nucleotide Polymorphism (SNPs), Indels, and other structural variants like Copy Number Variations (CNV)) thus, have a wide range of potential applications. These include identification of causative variants and the genes for genetic diseases, personalized genomics, population and evolutionary genetics, and forensic biology. This study represents two such applications of human variant analysis (particularly the analysis of SNPs and Indels). In the first chapter, SNPs were analyzed to understand the correlation between recombination rate and genetic diversity in the human genome, using a computational modeling program. A simulated human population was used to study the effect of various population level factors such as natural selective forces, the type of mutations, etc., on this correlation. In the second chapter, Next Generation Sequencing (in this case Whole Exome Sequencing) data and associated computational variant analysis tools and software were used to analyze both SNPs and Indels in the human genomes to find a lead candidate genetic variant responsible for Inherited Retinal Dystrophy in a family.
Alexei Fedorov (Committee Chair)
Robert Blumenthal (Committee Member)
Sadik Khuder (Committee Member)
102 p.
Bioinformatics; Biomedical Research; Evolution and Development; Genetics
SNP; Indel; Whole Exome Sequencing; Evolutionary Genetics; Population Genetics; Genetic Variant; Retinal Dystrophy; Next Generation Sequencing; Recombination Rate; Genetic Diversity; Natural Selection Forces; Mutation

Recommended Citations

Citations

  • Chakrabortty, S. (2017). SNPs and Indels Analysis in Human Genome using Computer Simulation and Sequencing Data [Master's thesis, University of Toledo]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=mco1501726874739045

    APA Style (7th edition)

  • Chakrabortty, Sharmistha. SNPs and Indels Analysis in Human Genome using Computer Simulation and Sequencing Data. 2017. University of Toledo, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=mco1501726874739045.

    MLA Style (8th edition)

  • Chakrabortty, Sharmistha. "SNPs and Indels Analysis in Human Genome using Computer Simulation and Sequencing Data." Master's thesis, University of Toledo, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=mco1501726874739045

    Chicago Manual of Style (17th edition)

mco1501726874739045
838
© 2017, all rights reserved.
This open access ETD is published by University of Toledo Health Science Campus and OhioLINK.