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De novo assembly of admixed South African genomes and its application in genetic susceptibility to tuberculosis.
Thesis (PhD)--Stellenbosch University, 2022.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2022
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| _version_ | 1867613900618334208 |
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| access_status_str | Open Access |
| author | Sparks, Anel |
| author2 | Moller, Marlo |
| author_browse | Moller, Marlo Sparks, Anel |
| author_facet | Moller, Marlo Sparks, Anel |
| author_sort | Sparks, Anel |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhD)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125164 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:43:29.841Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/125164 De novo assembly of admixed South African genomes and its application in genetic susceptibility to tuberculosis. Sparks, Anel Moller, Marlo Glanzmann, Brigitte Van der Spuy, Gian Tromp, Gerard Kinnear, Craig Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences. Molecular Biology and Human Genetics. Genomes Tuberculosis -- Susceptibility Intracellular pathogens Human immunogenetics UCTD Thesis (PhD)--Stellenbosch University, 2022. ENGLISH ABSTRACT: South Africa is a diverse country with populations of European, Asian, African, and mixed ancestry. A scourge on the health of South Africans of all ethnicities, is tuberculosis (TB). Although the infectious agent, Mycobacterium tuberculosis, is required for infection, the environment and human genetic component contributes to disease progression. TB susceptibility is a spectrum ranging from those who are completely resistant, to those who are susceptible to even the live attenuated vaccine. Identifying causal genetic variants in the latter group might increase knowledge on how the immune system fights intracellular pathogens, thereby informing genetic investigations of TB susceptibility in the general population. With a prevalence of over 1.8 million TB cases, Cape Town is an ideal area to conduct this research. South African diversity is represented here, but none are more so, than the South African Coloured (SAC) population. This heterogenous, five-way admixed population is the majority in the Western Cape province, and also the most prominent ethnicity in most medical genetics research projects in the region. In one form or another, genetic research will always require a reference genome. Currently, no such resource exists for the SAC population, despite evidence that this resource aids variant discovery if tailored to the cohort of interest. Such a resource requires high coverage sequencing of multiple individuals and subsequent interventions to create a chromosome level assembly. Additionally, any variant discovery made through a population-specific reference genome is isolated by that genome’s coordinate system. This means that findings cannot be related to other populations, nor can resources that depend on another coordinate system be used to aid the research. This study therefore set out to create a population-specific reference genome with the same coordinate system as the gold standard reference, while using minimal resources and with the aim to utilise it to diagnose an individual with Mendelian Susceptibility to Mycobacterium Disease (MSMD). Two individuals were sequenced using a short read approach and their data was used to assemble a rudimentary genome, SAC_scaf. These scaffolds were aligned to the gold standard reference genome, GRCh38, to determine the coordinates of the scaffolds within SAC_scaf. This alignment information was used to design PopPatch, an algorithm that converts sequences within a reference genome to population-specific ones based on the alignment information. As a result, SAC_PopPatch was constructed and evaluated. An individual with atypical susceptibility to TB was identified and whole genome sequencing data was obtained. These data were aligned to SAC_PopPatch as well as GRCh38 and variant call sets were prioritised in tandem. At the end of the prioritisation, the GRCh38 set yielded no discoveries, while the SAC_PopPatch set found a homozygous, nonsynonymous single nucleotide variant in exon 20 of the JAK1 gene. The discovery was due to the improved variant calling capabilities of the population-specific SAC_PopPatch combined with the GRCh38-based databases. The project successfully produced a novel approach that not only creates a population-specific reference genome from gappy assemblies, but also does so in a manner that maintains coordinate congruency with databases based on the gold standard reference genome. AFRIKAANSE OPSOMMING: Suid-Afrika se diversiteit is te danke aan die teenwoordigheid van populasies vanaf Europa, Asië en Afrika, asook gemengde individue. ’n Groot plaag wat tans Suid-Afrikaners se gesondheid beïnvloed, is tuberkulose (TB). Al is die patogeen, Mycobacterium tuberkulose, noodsaaklik vir infeksie, speel die persoon se omgewing en genetika ’n rol in hoe die siekte verloop. Die vatbaarheid vir TB is egter ’n spektrum wat aan die een kant mense het wat geheel beskerm is teen infeksie en aan die ander kant, mense wat selfs vatbaar is tot die verswakte entstof. Die laasgenoemde groep bied die geleentheid om kennis in te samel oor hoe ons immuunsisteme reageer op intrasellulêre patogene, en help sodoende om TB vatbaarheid in die algemene bevolking te verstaan. Met ’n TB voorkoms van meer as 1.8 miljoen, is Kaapstad die perfekte area vir hierdie navorsing. Die grootste diversiteit hier, is te sien in die Suid-Afrikaanse Kleurling (SAK) populasie. Hedendaagse SAK individue is vyf-rigting vermeng en is ook die meerderheid in die Wes-Kaap. As gevolg hiervan, is hulle ook prominente deelnemers aan studies wat betrekking het tot mediese genetika. Meeste genetiese navorsing maak van ’n verwysingsgenoom gebruik en tans is daar geen so ’n hulpbron vir die SAK populasie nie. Daar is ’n algemene verwysingsgenoom, maar navorsing het getoon dat die hulpbron beter werk as dit meer spesifiek is tot die gekose populasie. Ongelukkig, word hoë-dekking volgordebepaling van meervoudige individue benodig om so ’n hulpbron te skep. Daarbenewens, is die variante wat so gevind is ook nie vertaalbaar na ander populasies nie, aangesien hierdie variante geken word deur hul eie koördinate en nie oorstem met ander bronne nie. Die unieke koördinate beteken ook dat bevindinge en hulpbronne van ander studies nie gebruik kan word om navorsing in die gekose populasie te bevorder nie. Hierdie studie het daarom beoog om met minimale data en monsters ‘n verwysingsgenoom te skep wat ‘n koördinaatsisteem deel met die standaard genoom, GRCh38, en sodoende ’n variant te identifiseer wat moontlik die oorsaak is van ‘n pasiënt se vatbaarheid tot mikrobakteriese siektes. Twee gesonde individue is gekies om volgordebepaling te ondergaan en die data is gebruik om ‘n genoom te skep. Die genoom, SAC_scaf is daaropvolgens teen GRCh38 opgelyn om die koördinate van SAC_scaf se steierwerke te bepaal. Díe inligting is toe gebruik om PopPatch, ‘n algoritme wat volgordes in ‘n genoom omskakel na populasie data, te ontwerp en die resultaat was SAC_PopPatch. ‘n Pasiënt met oordrewe vatbaarheid tot TB is geïdentifiseer en het volgorde bepaling ondergaan. Hierdie data was opgelyn teen SAC_PopPatch, asook GRCh38 om genetiese variante te identifiseer. Die twee stelle variante is verder geprioritiseer, maar slegs die SAC_PopPatch stel was suksesvol. ‘n Homosigotiese, nie-sinonieme variant is ontdek in die 20ste ekson van die geen JAK1, te danke aan die gevorderde vermoë van SAC_PopPatch tesame met die toegang tot GRCh38 databasisse. Hierdie projek het ‘n nuwe metode te ontwikkel wat nie net swak genoomsamestellings kan benut nie, maar ook hou by ‘n gewilde koördinaat sisteem. Doctoral 2022-01-17T12:29:46Z 2022-04-29T12:56:50Z 2023-01-04T03:00:10Z 2022-01 Thesis http://hdl.handle.net/10019.1/125164 en_ZA Stellenbosch University xxii, 134 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Genomes Tuberculosis -- Susceptibility Intracellular pathogens Human immunogenetics UCTD Sparks, Anel De novo assembly of admixed South African genomes and its application in genetic susceptibility to tuberculosis. |
| title | De novo assembly of admixed South African genomes and its application in genetic susceptibility to tuberculosis. |
| title_full | De novo assembly of admixed South African genomes and its application in genetic susceptibility to tuberculosis. |
| title_fullStr | De novo assembly of admixed South African genomes and its application in genetic susceptibility to tuberculosis. |
| title_full_unstemmed | De novo assembly of admixed South African genomes and its application in genetic susceptibility to tuberculosis. |
| title_short | De novo assembly of admixed South African genomes and its application in genetic susceptibility to tuberculosis. |
| title_sort | de novo assembly of admixed south african genomes and its application in genetic susceptibility to tuberculosis |
| topic | Genomes Tuberculosis -- Susceptibility Intracellular pathogens Human immunogenetics UCTD |
| url | http://hdl.handle.net/10019.1/125164 |
| work_keys_str_mv | AT sparksanel denovoassemblyofadmixedsouthafricangenomesanditsapplicationingeneticsusceptibilitytotuberculosis |