Bioinformatics in Africa: The Rise of Ghana?
Ontology highlight
ABSTRACT:
SUBMITTER: Karikari TK
PROVIDER: S-EPMC4574930 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming. This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and the Wellcome Trust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations.
| S-EPMC4364068 | biostudies-literature
Project description:Adapting community-based protected areas to local context and evaluating their success across a range of possible socio-economic and ecological outcomes depends, in part, on understanding the perceptions of local actors. This article presents results from a mixed methods study that focuses on how and why religious identity, a prominent aspect of Ghanaian culture, is related to perceptions of the performance of several Community Resource Management Areas (CREMAs). CREMAs are a form of Ghanaian protected area that emphasizes community participation and a range of socio-economic and ecological objectives. Using importance-satisfaction analysis, large-scale survey results show that respondents that identify as Christians consistently assign greater importance to CREMA outcomes than do those that identify with Traditional religions. Education and whether respondents were native to an area (both of which were correlated with religious identity) were also systematically related to perceptions of CREMA importance, with those that are educated and non-native to an area tending to assign higher importance to CREMA outcomes. Follow up focus group participants from the Avu Lagoon CREMA suggest that the patterns result from differing 'openness' to new ideas, relative dependence on natural resources, acceptance of Traditional practices associated with conservation, and a sense, for some, that ecological conditions are divinely ordained. Christianity, education and non-nativity are associated with much larger performance gaps, particularly with respect to socio-economic impacts. The article concludes with a discussion of the implications for conservation interventions and the use of perceptions in assessing protected area performance.
| S-EPMC5886562 | biostudies-literature
Project description:Helminths are among the most widespread infectious agents prevalent in tropical and sub-tropical regions of the developing world defined by inadequate sanitation, poverty and unsafe water sources. This study was carried out to describe the distribution of helminth and malaria parasite infections in the middle-belt of Ghana in sub-Saharan Africa where disease burden, including anaemia is rife and helminths are perceived to be significant contributors of the burden.A cross-sectional survey involving 1826 residents located in the middle belt of Ghana where no or very little previous community-based helminth work had been carried out. The participants randomly recruited at household level provided biological samples collected over a 12-month period following a rigorous consenting process and these were analysed to describe the different types and seasonal distribution of helminths.Overall, 19.3% intestinal helminth infection prevalence was documented. Also based on parasites targeted for elimination, 12.1% Hookworm, 4.0% Hymenolepis nana/Hymenolepis dimunita, 1.5% Ascaris lumbricoides, 1.5% Taenia species, 0.9% Strongyloides stercoralis and 0.8% Trichuris trichiura, with about 1.0% polyphelminthiasis were recorded in the survey. About 55.4% and 44.4% of the participants had heavy hookworm and Trichuris infections respectively. Most of the Ascariasis (83.3%) infections were light in intensity. Hookworm infection was identified with significant odds considering decreasing age (OR?=?2.09, p?=?0.03), inappropriate footwear use (OR?=?1.88, p?=?0.021), malaria parasite co-infection (OR?=?1.62, p?=?0.018), not scrubbing nails during hand washing (OR?=?0.68, p?=?0.048), source of drinking water (OR?=?2.51, p?=?0.027) and religion (OR?=?4.36, p?=?0.002).Hookworm infection was significantly higher in younger age groups and among those who did not have safe drinking water. Proper sanitation, protective footwear, religion and good personal hygiene practices were found to influence helminth and hookworm prevalence in the area. Malaria parasite coinfection with helminths, especially hookworm infections increased 2-fold.
| S-EPMC6020085 | biostudies-other
Project description:The article elaborates on the program highlights of the 3rd African Student Council Symposium 2019. The one-day symposium was held in Kwame Nkrumah University of Science and Technology (KNUST), Ghana, on 11 November 2019 during the 6th joint international bioinformatics conference of the ISCB and ASBCB. It consisted of three sessions that included keynote talks by Prof Christine Orengo and Dr. Amel Ghouila, and seven selected student speaker talks from different areas of bioinformatics. The students benefited from networking and learning about ongoing research work by their peers hailing from different countries of the African region. The symposium proved to be pivotal to strengthen connections in the African bioinformatics student community.
| S-EPMC7255899 | biostudies-literature
Project description:Post-apartheid South Africa has seen an unprecedented rise and fall of mortality in less than two decades as a result of the HIV/AIDS epidemic and the subsequent rollout of free antiretroviral therapy (ART). Since the incidence of both was not equal for rich and poor, it is likely to also have affected disparities in health and survival chances by income. We use large nationwide surveys for 2001, 2007 and 2011 to obtain estimates of average income and mortality at the aggregate level of a municipality, and then to examine changes in mortality - and in inequality in mortality by income ─ over time. Using concentration indices to measure health inequality, we demonstrate that both the mean mortality level and absolute inequality in mortality by income rose rapidly until 2006, and declined again sharply since the rollout of free ART. Relative inequalities in mortality by income, however, remained fairly stable over the 2001-2011 period. The analysis of age-sex-specific mortality rates shows that it was in particular for adults aged 18-59 years that mortality and absolute inequality increased substantially between 2001 and 2006, followed by a rapid drop thereafter. These trends were far more pronounced for males than females. This means that the HIV/AIDS epidemic has taken a serious death toll, which was concentrated disproportionately among the poorest segments of the population and especially affected (older) males. While South Africa has been very successful in curbing the overall mortality trend since 2006, large disparities in survival prospects by income, race and gender continue to exist. Targeted efforts are required if it wants to further reduce the very unequal chances of living to old age for richer and poorer population groups of all ages.
| S-EPMC6077134 | biostudies-literature
Project description:The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R and Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping. The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed that the ADP of Ghana has both European and Asian genetic signatures. The ADP also displays considerable variation in the MC1R gene. Black coat colour is the most predominant within the breed, with the dominant black alleles of both Asian and European origin contributing to the majority of alleles in the pool. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. Other colour variants may be due to epistatic interactions with additional coat colour loci, or mutations. The wide variations in coat colour patterns suggest that morphology alone cannot be used to adequately characterise Ghanaian local pigs. PCA analysis of SNP genotyping data revealed a strong location effect on clustering of local Ghanaian pigs. Based on this work, we recommend that further studies be carried out on more local pigs to find out the effect of admixture on important adaptive and economic traits of the ADP and other local Sus breeds in Africa to help develop a sustainable conservation programmes to prevent the decline of this genetic resource.
2017-03-08 | GSE84604 | GEO
Project description:BACKGROUND AND OBJECTIVES:Early bystander cardiopulmonary resuscitation (CPR) is one of the most important predictors of out-of-hospital cardiac arrests (OHCA) survival. There is a dearth of literature on CPR engagement in countries such as Ghana, where cardiovascular events are increasingly prevalent. In this study, we sought to evaluate Ghanaians' knowledge of and attitudes towards bystander CPR, in the context of the country's nascent emergency medicine network. METHODS:Capitalizing on the growing ubiquity and use of social media across the country, we used a novel social media sampling strategy for this study. We created, pre-tested, and distributed an online survey, using the two most utilized social media platforms in Ghana: WhatsApp and Facebook. An airtime data incentive of 5 US dollars, worth between 5 and 10 GB of cellular data based on mobile phone carrier, was provided as incentive. Inclusion criteria were (1) ? 18 years of age, (2) living in Ghana. Survey participants were encouraged to distribute the survey within their own networks to expand its reach. We stratified participants' responses by healthcare affiliation, and further grouped healthcare workers into ambulance and non-ambulance personnel. We used chi-square (?2)/Fisher's Exact tests to compare differences in responses between the groups. Based on the question "have you ever heard of CPR?", an alpha of 0.05 and a 95% confidence interval, we expected to have 80% power to detect a 15% difference in responses between lay and healthcare providers with an estimated sample size of 246 study participants. RESULTS:The survey was launched on 8 July 2019 and closed approximately 51 h post-launch. With a 64% completion rate and 479 unique survey completions, the study was overpowered at 96% power, to detect differences in responses between the groups. There was geographic representation across all 10 historic regions of Ghana. Over half (57.8%, n = 277) of the respondents were non-medically affiliated, and 71.9% were women. Healthcare workers were more aware of CPR than lay respondents (96.5% vs 68.1%; p < 0.001). Eighty-five percent of respondents were aware that CPR involves chest compressions, and almost 70% indicated that "mouth to mouth" is a necessary component of CPR. Fewer than 10% were unwilling to administer CPR. Lack of skills (44.9%) and fear of causing harm (25.5%) were barriers noted by respondents for not administering CPR. Notably, a quarter of ambulance workers reported never having received CPR training. If they were to witness a collapse, 62.0% would call an ambulance, and 32.6% would hail a taxi. CONCLUSION:The majority of participants are willing to perform CPR. Contextualized training that emphasizes hands-only CPR and builds participants' confidence may increase bystander willingness and engagement.
| S-EPMC7288511 | biostudies-literature
Project description:Little is known about the relationship between self-identified difficulties conceiving, biomedical infertility, and union instability in Sub-Saharan Africa. Previous research suggests that infertility increases the risk of psychological distress and marital conflict, encourages risky sexual behaviour, and deprives infertile individuals and couples of an important source of economic and social capital. Qualitative research has suggested that there may be a link between infertility and divorce; less is known about the implications of infertility for unmarried couples. In this paper, discrete-time hazard models are applied to 8 waves of secondary panel data from Ghana collected by the Population Council of New York and the University of Cape Coast (pooled n = 10,418) between 1998 and 2004. Results show a positive relationship between perceived difficulties conceiving and relationship instability for both married women and those in non-marital sexual unions; this relationship, however, does not hold for biomedical infertility. Future research should examine this relationship using nationally representative data in a cross-national comparison to determine whether results hold across the subcontinent.
| S-EPMC6241086 | biostudies-literature
Project description:The fate of hunting and gathering populations following the rise of agriculture and pastoralism remains a topic of debate in the study of human prehistory. Studies of ancient and modern genomes have found that autochthonous groups were largely replaced by expanding farmer populations with varying levels of gene flow, a characterization that is influenced by the almost universal focus on the European Neolithic.1-5 We sought to understand the demographic impact of an ongoing cultural transition to farming in Southwest Ethiopia, one of the last regions in Africa to experience such shifts.6 Importantly, Southwest Ethiopia is home to several of the world's remaining hunter-gatherer groups, including the Chabu people, who are currently transitioning away from their traditional mode of subsistence.7 We generated genome-wide data from the Chabu and four neighboring populations, the Majang, Shekkacho, Bench, and Sheko, to characterize their genetic ancestry and estimate their effective population sizes over the last 60 generations. We show that the Chabu are a distinct population closely related to ancient people who occupied Southwest Ethiopia >4,500 years ago. Furthermore, the Chabu are undergoing a severe population bottleneck, which began approximately 1,400 years ago. By analyzing eleven Eastern African populations, we find evidence for divergent demographic trajectories among hunter-gatherer-descendant groups. Our results illustrate that although foragers respond to encroaching agriculture and pastoralism with multiple strategies, including cultural adoption of agropastoralism, gene flow, and economic specialization, they often face population decline.
| S-EPMC9050894 | biostudies-literature
Project description: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 adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network's Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.
| S-EPMC7194140 | biostudies-literature