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Rarefaction as a tool to determine variant diversity in monogenetic disorders
Dissertation (MSc)--University of Pretoria, 2015.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2016
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| _version_ | 1867613641058025472 |
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| access_status_str | Open Access |
| author2 | Pepper, Michael Sean |
| author_browse | Pepper, Michael Sean |
| author_facet | Pepper, Michael Sean |
| collection | Thesis |
| dc_rights_str_mv | © 2016 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. |
| description | Dissertation (MSc)--University of Pretoria, 2015. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/53050 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:39:22.254Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/53050 Rarefaction as a tool to determine variant diversity in monogenetic disorders Pepper, Michael Sean jeanne.vrensburg@gmail.com Alessandrini, Marco Van Rensburg, Jeanne UCTD Genetic diversity Mathematical models Disease-associated variants Monogenic disorders Cystic fibrosis (CF) Metachromatic leukodystrophy (MLD) Shannon-Weaver index Simpson Diversity index Rarefaction diversity Genetic disorders Healthcare Health sciences theses SDG-03 SDG-03: Good health and well-being Health sciences theses SDG-04 SDG-04: Quality education Health sciences theses SDG-17 SDG-17: Partnerships for the goals Dissertation (MSc)--University of Pretoria, 2015. Genetic diversity is a well-described concept within many biological disciplines. However, mathematical models determining genetic diversity are often applied within ecological disciplines and are rarely explored within the medical field. Given that genetically associated disorders and complications can occur at high frequency in developing countries, the primary aim of this study was to determine whether or not diversity theory could be applied to disease-associated variants. Two monogenic disorders were selected for this purpose one commonly observed disorder known as cystic fibrosis (CF), and one rare disorder known as metachromatic leukodystrophy (MLD). Despite being a common monogenic disorder, the clinical and molecular presentation of CF in the different population groups of South Africa is largely unknown. Thus, the medical records of 45 CF patients attending the Steve Biko Academic Hospital CF clinic were investigated to better understand the manifestation of this disorder in these patients. Additionally, molecular data was collected for both CF and MLD through published reports and analysed via the Shannon-Weaver, Simpson, Simpson Diversity, and rarefaction diversity methods. The rarefaction method was found to be the most informative measure of diversity and a potentially powerful tool to employ in the development and/or refinement of population-specific screening panels. em2025 Immunology MSc Unrestricted SDG-03: Good health and well-being SDG-04: Quality education SDG-17: Partnerships for the goals 2016-06-10T07:18:42Z 2016-06-10T07:18:42Z 2016-04-22 2015 Dissertation Van Rensburg, J 2015, Rarefaction as a tool to determine variant diversity in monogenetic disorders, MSc Dissertation, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/53050> A2016 http://hdl.handle.net/2263/53050 en © 2016 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. application/pdf University of Pretoria |
| spellingShingle | UCTD Genetic diversity Mathematical models Disease-associated variants Monogenic disorders Cystic fibrosis (CF) Metachromatic leukodystrophy (MLD) Shannon-Weaver index Simpson Diversity index Rarefaction diversity Genetic disorders Healthcare Health sciences theses SDG-03 SDG-03: Good health and well-being Health sciences theses SDG-04 SDG-04: Quality education Health sciences theses SDG-17 SDG-17: Partnerships for the goals Rarefaction as a tool to determine variant diversity in monogenetic disorders |
| title | Rarefaction as a tool to determine variant diversity in monogenetic disorders |
| title_full | Rarefaction as a tool to determine variant diversity in monogenetic disorders |
| title_fullStr | Rarefaction as a tool to determine variant diversity in monogenetic disorders |
| title_full_unstemmed | Rarefaction as a tool to determine variant diversity in monogenetic disorders |
| title_short | Rarefaction as a tool to determine variant diversity in monogenetic disorders |
| title_sort | rarefaction as a tool to determine variant diversity in monogenetic disorders |
| topic | UCTD Genetic diversity Mathematical models Disease-associated variants Monogenic disorders Cystic fibrosis (CF) Metachromatic leukodystrophy (MLD) Shannon-Weaver index Simpson Diversity index Rarefaction diversity Genetic disorders Healthcare Health sciences theses SDG-03 SDG-03: Good health and well-being Health sciences theses SDG-04 SDG-04: Quality education Health sciences theses SDG-17 SDG-17: Partnerships for the goals |
| url | http://hdl.handle.net/2263/53050 |