Gerrit Reinier Botha

University of Cape Town | UCT

Structural variants are responsible for a large part of genomic variation between individuals and play a role in both common and rare diseases. Databases cataloguing structural variants notably do not represent the full spectrum of global diversity, particularly missing information from most African populations. To address this representation gap,...

Background and Objectives Amyotrophic lateral sclerosis (ALS) is a degenerative condition of the brain and spinal cord in which protein-coding variants in known ALS disease genes explain a minority of sporadic cases. There is a growing interest in the role of noncoding structural variants (SVs) as ALS risk variants or genetic modifiers of ALS pheno...

Based on evaluations of imputation performed on a genotype dataset consisting of about 11,000 sub-Saharan African (SSA) participants, we show Trans-Omics for Precision Medicine (TOPMed) and the African Genome Resource (AGR) to be currently the best panels for imputing SSA datasets. We report notable differences in the number of single-nucleotide po...

Background: Genome‑wide association studies (GWAS) are a powerful method to detect associations between variants and phenotypes. A GWAS requires several com‑ plex computations with large data sets, and many steps may need to be repeated with varying parameters. Manual running of these analyses can be tedious, error‑prone and hard to reproduce. Resu...

Background Genome-wide association studies (GWAS) are a powerful method to detect associations between variants and phenotypes. A GWAS requires several complex computations with large datasets, and many steps may need to be repeated with varying parameter. Manual running of these analyses can be tedious, error-prone and hard to reproduce. Results...

Chloroquine/hydroxychloroquine have been proposed as potential treatments for COVID-19. These drugs have warning labels for use in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Analysis of whole genome sequence data of 458 individuals from sub-Saharan Africa showed significant G6PD variation across the continent. We identifi...

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03286-9.

Introduction: Investigating variation in genes involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs are key to characterizing pharmacogenomic (PGx) relationships. ADME gene variation is relatively well characterized in European and Asian populations, but data from African populations are under-studied—which has implic...

Human immunodeficiency virus (HIV) infection remains a significant public health burden globally. The role of viral co-infection in the rate of progression of HIV infection has been suggested but not empirically tested, particularly among children. We extracted and classified 42 viral species from whole-exome sequencing (WES) data of 813 HIV-infect...

With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependenci...

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized primarily by progressive loss of motor neurons. Although ALS occurs worldwide and the frequency and spectrum of identifiable genetic causes of disease varies across populations, very few studies have included African subjects. In addition to a hexanucleotide repe...

For the past 20 years the recombination detection program (RDP) project has focused on the development of a fast, flexible and easy to use Windows-based recombination analysis tool. Whereas previous versions of this tool have relied on considerable user-mediated verification of detected recombination events, the latest iteration, RDP5, is automated...

Investigating variation in genes involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs are key to characterising pharmacogenomic (PGx) relationships. ADME gene variation is relatively well characterised in European and Asian populations, but African populations are under-studied -- which has implications for safe and e...

Chloroquine/hydroxychloroquine have been proposed as potential treatments for COVID-19. These drugs have warning labels for use in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Analysis of whole-genome sequence data of 458 individuals from sub-Saharan Africa showed significant G6PD variation across the continent. We identifi...

Vroue van Afrika-afkoms is meer vatbaar vir bakteriële vaginose (BV) in vergelyking met Europese vroue. Beide mikrobiese diversiteit (soos met BV) sowel as spesifieke bakteriële taksa speel ‘n rol in seksuele en reproduktiewe gesondheid insluitende MIV vatbaarheid. Die moontlike rol van geografi ese ligging en etnisiteit op die verhouding tussen mi...

Objective Findings from animal studies indicate that the early gut bacteriome is a potential mechanism linking maternal prenatal stress with health trajectories in offspring. However, clinical studies are scarce and the associations of maternal psychological profiles with the early infant faecal bacteriome is unknown. This study aimed to investigat...

Human genomic data are large and complex, and require adequate infrastructure for secure storage and transfer. The NIH and The Wellcome Trust have funded multiple projects on genomic research, including the Human Heredity and Health in Africa (H3Africa) initiative, and data are required to be deposited into the public domain. The European Genome-ph...

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines ada...

Background: Findings from animal studies indicate that the early gut bacteriome is a potential mechanism linking maternal prenatal stress with health trajectories in offspring. However, clinical studies are scarce and the associations of maternal psychological profiles with the early infant faecal bacteriome is unknown. This study aimed to investig...

Background: The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to study and...

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines ada...

There are limited data on meconium and faecal bacterial profiles from African infants and their mothers. We characterized faecal bacterial communities of infants and mothers participating in a South African birth cohort. Stool and meconium specimens were collected from 90 mothers and 107 infants at birth, and from a subset of 72 and 36 infants at 4...

Young African females are at increased risk of HIV acquisition, and genital inflammation or the vaginal microbiome may contribute to this risk. We studied these factors in 168 HIV negative South African adolescent women aged 16-22 years. Unsupervised clustering of 16S rRNA gene sequences revealed three clusters (subtypes), one of which was strongly...

The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeast...

Young South African women, from resource-poor communities, face several sexual and reproductive health challenges. Here we describe the vaginal microbiota and sexually transmitted infection (STI) prevalence of 102; 16–22-year-old, HIV-negative South African women from a low-income, high-population-density community in Cape Town (CPT). Vaginal micro...

OpsommingJong Suid-Afrikaanse vroue uit hulpbron-arm gemeenskappe staar verskeie uitdagings in die gesig in terme van hulle seksuele en reproduktiewe gesondheid. Hier beskryf ons die voorkoms van vaginale mikrobiota en seksueel oordraagbare infeksies (SOI’s) onder 102; 16–22-jarige MIV-negatiewe Suid-Afrikaanse vroue uit ’n lae-inkomste, hoë-bevolk...

The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a fram...

Background: The biomedical prevention of HIV transmission that medical male circumcision confers was confirmed by three clinical trial setting and then rolled out in VMMC programs in sub-Saharan Africa. Data assessing the effectiveness of this under programmatic conditions is not available. Concerns about possible risk compensation in circumcised m...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outp...

In the context of recent international initiatives to bolster genomics research for Africa, and more specifically to develop bioinformatics expertise and networks across the continent, a workshop on computational metagenomics was organized during the end of 2014 at the University of Mauritius. The workshop offered background on various aspects of c...

Family, adoption and twin studies strongly suggest that bipolar disorder (BD) has a genetic component, with heritability estimates as high as 85%. The aim of this study was to identify BD susceptibility variants using whole-genome technologies in a large Afrikaner family affected with BD. Whole-genome sequencing was performed on four related indivi...

The classification accuracy of text-based language identification depends on several factors, including the size of the text fragment to be identified, the amount of training data available, the classification features and algorithm employed, and the similarity of the languages to be identified. To date, no systematic study of these factors and the...

The authors investigate the performance of text-based language identification systems on the 11 official languages of South Africa, when n-gram statistics are used as features for classification. In particular, the authors compare support vector machines (SVMs) and likelihood-based classifiers on different amounts of input text, both from a closed...

Two methods for objectively measuring similarities and dissimilarities between the eleven official languages of South Africa are described. The first concerns the use of n-grams. The confusions between different languages in a text-based language identification system can be used to derive information on the relationships between the languages. Our...

Many applications of pattern recognition to natural lan-guage processing require large text corpora in a speci-fied language. For many of the languages of the world, such corpora are not readily available, but significant quantities of text are available on the World Wide Web. We describe and compare two approaches to gathering language-specific co...