Functional Genome-wide Association Studies (fGWAS) and genomics landscape of signatures of polygenic adaptation in Botswana populations with HIV-1 C infection
type: CreativeWork
description: The burden of the human immunodeficiency virus subtype (HIV) is catastrophic, especially in Botswana, a nation in Southern Africa, where 20.7% of persons aged 15 to 49 years are living with HIV (PWH). Although HIV exposure rates are extremely high, individual differences in clinical outcomes point to the importance of host genetic variables. Genome-wide association studies (GWAS) are methods widely used for identifying single nucleotide polymorphisms (SNPs) linked to different phenotypes such as HIV-1 subtype C (HIV-1C) susceptibility or resistance. Even though, conventional GWAS techniques alone cannot illuminate the associated functional pathways beyond detecting association SNPs. Alternatively, functional genome-wide association studies (fGWAS), which are post-GWAS analyses, can be utilized to put GWAS summary results into functional context. We hereby, first describe the fGWAS employing whole genome sequences (WGS) of Batswana exposed to HIV-1C. Although autosomal SNPs are widely utilized for functional-GWAS research, recent studies have also linked mitochondria DNA (mtDNA) haplotypes to various HIV outcomes. We explored the possibility of using both autosomal and mtDNA SNPs to enrich fGWAS analysis. On another hand, people from Botswana (collectively called Batswana) exhibits a homogenous genetic structure and has also been identified as the closest population to the most recent common ancestor (MRCA) of human species. Concomitantly the population has extremely high HIV1C burden. It remains unclear if increased susceptibility to HIV-1C infection may be associated with its closeness to the ancestral genomes. We investigated the genomics landscape of signatures of polygenic adaptation to the HIV-1C in Botswana using genomewide scans for selection (GWSS). For the first goal, we looked at several HIV-related studies that had been done in Botswana from 1995 to 2020. We saw significant advancements in the fight against the pandemic, including the early introduction o…
abstract: The burden of the human immunodeficiency virus subtype (HIV) is catastrophic, especially in Botswana, a nation in Southern Africa, where 20.7% of persons aged 15 to 49 years are living with HIV (PWH). Although HIV exposure rates are extremely high, individual differences in clinical outcomes point to the importance of host genetic variables. Genome-wide association studies (GWAS) are methods widely used for identifying single nucleotide polymorphisms (SNPs) linked to different phenotypes such as HIV-1 subtype C (HIV-1C) susceptibility or resistance. Even though, conventional GWAS techniques alone cannot illuminate the associated functional pathways beyond detecting association SNPs. Alternatively, functional genome-wide association studies (fGWAS), which are post-GWAS analyses, can be utilized to put GWAS summary results into functional context. We hereby, first describe the fGWAS employing whole genome sequences (WGS) of Batswana exposed to HIV-1C. Although autosomal SNPs are widely utilized for functional-GWAS research, recent studies have also linked mitochondria DNA (mtDNA) haplotypes to various HIV outcomes. We explored the possibility of using both autosomal and mtDNA SNPs to enrich fGWAS analysis. On another hand, people from Botswana (collectively called Batswana) exhibits a homogenous genetic structure and has also been identified as the closest population to the most recent common ancestor (MRCA) of human species. Concomitantly the population has extremely high HIV1C burden. It remains unclear if increased susceptibility to HIV-1C infection may be associated with its closeness to the ancestral genomes. We investigated the genomics landscape of signatures of polygenic adaptation to the HIV-1C in Botswana using genomewide scans for selection (GWSS). For the first goal, we looked at several HIV-related studies that had been done in Botswana from 1995 to 2020. We saw significant advancements in the fight against the pandemic, including the early introduction o…
author: Choga, Wonderful Tatenda
keywords: Human Genetics
date published: 2022
date modified: 2026-07-22T22:22:37Z
provider: University of Cape Town
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Department of Pathology

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property ID: Handle
value: http://hdl.handle.net/11427/37108