The African Society of Human Genetics successfully launches global data science workshops.

To accelerate the impact of African genomics on human health, data science skills and awareness of Africa's rich genetic diversity must be strengthened globally. We describe the first African genomics data science workshop, implemented by the African Society of Human Genetics (AfSHG) and international partners, providing a framework for future workshops.

IHP-PING-generating integrated human protein-protein interaction networks on-the-fly.

Advances in high-throughput sequencing technologies have resulted in an exponential growth of publicly accessible biological datasets. In the 'big data' driven 'post-genomic' context, much work is being done to explore human protein-protein interactions (PPIs) for a systems level based analysis to uncover useful signals and gain more insights to advance current knowledge and answer specific biological and health questions. These PPIs are experimentally or computationally predicted, stored in different online databases and some of PPI resources are updated regularly. As with many biological datasets, such regular updates continuously render older PPI datasets potentially outdated. Moreover, while many of these interactions are shared between these online resources, each resource includes its own identified PPIs and none of these databases exhaustively contains all existing human PPI maps. In this context, it is essential to enable the integration of or combining interaction datasets from different resources, to generate a PPI map with increased coverage and confidence. To allow researchers to produce an integrated human PPI datasets in real-time, we introduce the integrated human protein-protein interaction network generator (IHP-PING) tool. IHP-PING is a flexible python package which generates a human PPI network from freely available online resources. This tool extracts and integrates heterogeneous PPI datasets to generate a unified PPI network, which is stored locally for further applications.

Assent, parental consent and reconsent for health research in Africa: thematic analysis of national guidelines and lessons from the SickleInAfrica registry.

The enrolment of children and adolescents in health research requires that attention to be paid to specific assent and consent requirements such as the age range for seeking assent; conditions for parental consent (and waivers); the age group required to provide written assent; content of assent forms; if separate assent and parental consent forms should be used, consent from emancipated young adults; reconsent at the age of adulthood when a waiver of assent requirements may be appropriate and the conditions for waiving assent requirements. There is however very little available information for researchers and ethics committees on how to navigate these different issues. To provide guidance to research initiatives, the SickleInAfrica consortium conducted a thematic analysis of a sample of research ethics guidelines and procedures in African countries, to identify guidance for assent requirements in health research. The thematic analysis revealed that 12 of 24 African countries specified the age group for which assent is required. The minimum age for written assent varied across the countries. Five countries, Algeria, Botswana, Cameroon, Nigeria and The Democratic Republic of Congo require consent from both parents/family council in certain circumstances. Botswana, Nigeria, South Africa and Uganda have specific assent/consent requirements for research with emancipated minors. South Africa and Algeria requires re-consent at onset of adulthood. Five countries (Botswana, Cameroon, Nigeria, South Africa and Tanzania) specified conditions for waiving assent requirements. The CIOMS and the ICH-GCP guidelines had the most comprehensive information on assent requirements compared to other international guidelines. An interactive map with assent requirements for different African countries is provided. The results show a major gap in national regulations for the inclusion of minors in health research. The SickleInAfrica experience in setting up a multi-country SCD registry in Africa highlights the need for developing and harmonising national and international guidelines on assent and consent requirements for research involving minors. Harmonisation of assent requirements will help facilitate collaborative research across countries.

Utilization of Pneumococcal Vaccine and Penicillin Prophylaxis in Sickle Cell Disease in Three African Countries: Assessment among Healthcare Providers in SickleInAfrica.

Sickle cell disease is a genetic disease with a predisposition to infections caused by encapsulated organisms, especially Streptococcus pneumoniae. Pneumococcal vaccines and prophylactic penicillin have reduced the rate of this infection and mortality in sickle cell disease. However, implementation of these interventions is limited in Africa. The objectives of the study were to assess health care providers' behaviors with the implementation of pneumococcal vaccination and penicillin prophylaxis and to identify barriers to their use. A 25-item online questionnaire was administered through SickleinAfrica: a network of researchers, and healthcare providers, in Ghana, Nigeria, and Tanzania, working to improve health outcomes of sickle cell disease in Africa. Data was collected and managed using the Research Electronic Data Capture (REDCap), tools and data analysis was done using STATA version 13 and R statistical software. Eighty-two medical practitioners responded to the questionnaire. Only 54.0 and 48.7% of respondents indicated the availability of published guidelines on sickle cell disease management and pneumococcal vaccine use, respectively, at their facilities. The majority (54.0%) perceived that the vaccines are effective but over 20.0% were uncertain of their usefulness. All respondents from Ghana and Tanzania affirmed the availability of guidelines for penicillin prophylaxis in contrast to 44.1% in Nigeria. Eighty-five percent of respondents affirmed the need for penicillin prophylaxis but 15.0% had a contrary opinion for reasons including the rarity of isolation of Streptococcus pneumoniae in African studies, and therefore, the uncertainty of its benefit. Lack of published guidelines on the management of sickle cell disease and doubts about the necessity of prophylactic measures are potential barriers to the implementation of effective interventions.

The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research.

BACKGROUND: Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)'s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation. RESULTS: The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD. CONCLUSION: To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond.

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.

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 framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

Application of Genomic Medicine in Africa: 14th Conference of the African Society of Human Genetics and the 2nd International Congress of the Moroccan Society of Genomics and Human Genetics, Rabat, Morocco 2022.

The 14th African Society of Human Genetics (AfSHG) Morocco Meeting and 2nd International Congress of the Moroccan Society of Genomics and Human Genetics (SM2GH), held in Rabat, Morocco, from December 12 through 17, 2022, brought together 298 attendees from 23 countries, organized by the AfSHG in collaboration with the SM2GH. The conference's overarching theme was "Applications of Genomics Medicine in Africa," covering a wide range of topics, including population genetics, genetics of infectious diseases, hereditary disorders, cancer genetics, and translational genetics. The conference aimed to address the lag in the field of genetics in Africa and highlight the potential for genetic research and personalized medicine on the continent. The goal was to improve the health of African populations and global communities while nurturing the careers of young African scientists in the field. Distinguished scientists from around the world shared their recent findings in genetics, immunogenetics, genomics, genome editing, immunotherapy, and ethics genomics. Precongress activities included a 2-day bioinformatics workshop, "NGS Analysis for Monogenic Disease in African Populations," and a Young Investigators Forum, providing opportunities for young African researchers to showcase their work. The vast genetic diversity of the African continent poses a significant challenge in investigating and characterizing public health issues at the genetic and functional levels. Training, research, and the development of expertise in genetics, immunology, genomics, and bioinformatics are vital for addressing these challenges and advancing genetics in Africa. The AfSHG is committed to leading efforts to enhance genetic research, coordinate training, and foster research collaborations on the continent.

Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem.

We previously proposed a structure for recording consent-based data use 'categories' and 'requirements' - Consent Codes - with a view to supporting maximum use and integration of genomic research datasets, and reducing uncertainty about permissible re-use of shared data. Here we discuss clarifications and subsequent updates to the Consent Codes (v4) based on new areas of application (e.g., the neurosciences, biobanking, H3Africa), policy developments (e.g., return of research results), and further practical considerations, including developments in automated approaches to consent management.

Developing Clinical Phenotype Data Collection Standards for Research in Africa.

Modern biomedical research is characterised by its high-throughput and interdisciplinary nature. Multiproject and consortium-based collaborations requiring meaningful analysis of multiple heterogeneous phenotypic datasets have become the norm; however, such analysis remains a challenge in many regions across the world. An increasing number of data harmonisation efforts are being undertaken by multistudy collaborations through either prospective standardised phenotype data collection or retrospective phenotype harmonisation. In this regard, the Phenotype Harmonisation Working Group (PHWG) of the Human Heredity and Health in Africa (H3Africa) consortium aimed to facilitate phenotype standardisation by both promoting the use of existing data collection standards (hosted by PhenX), adapting existing data collection standards for appropriate use in low- and middle-income regions such as Africa, and developing novel data collection standards where relevant gaps were identified. Ultimately, the PHWG produced 11 data collection kits, consisting of 82 protocols, 38 of which were existing protocols, 17 were adapted, and 27 were novel protocols. The data collection kits will facilitate phenotype standardisation and harmonisation not only in Africa but also across the larger research community. In addition, the PHWG aims to feed back adapted and novel protocols to existing reference platforms such as PhenX.

Investigation into the use of short message services to expand uptake of human immunodeficiency virus testing, and whether content and dosage have impact.

OBJECTIVE: South Africa has one of the highest human immunodeficiency virus (HIV) prevalence rates in the world, but despite the well-established benefits of HIV counseling and testing (HCT), there is low uptake of HCT. The study aimed to investigate the effectiveness of using short message services (SMSs) to encourage HCT while interrogating the impact of altering SMS content and dosage (the number of SMSs). MATERIALS AND METHODS: About 2,533 participants were recruited via an SMS sent to 24,000 mobiles randomly sampled from a pre-existing database. Recruits were randomly allocated to four intervention groups that received 3 or 10 informational (INFO) or motivational (MOTI) SMSs, and a control group. After the intervention, participants were prompted to go for HCT, and postintervention assessment was done after 3 weeks. RESULTS: In comparison with the control, receipt of 10 MOTI messages had the most impact on uptake of HCT with a 1.7-fold increased odds of testing (confidence interval 95%; p=0.0036). The lack of efficacy of three SMSs indicates a threshold effect, that is, a minimum number of MOTI SMSs is required. INFO SMSs, whether 3 or 10 were sent, did not have a statistically significant effect. The cost can be calculated for the marginal effect of the SMSs, that is, the cost to get people to test over and above those who were likely to test without the intervention. Use of 10 MOTI SMSs yielded a cost-per-tester of $2.41. CONCLUSIONS: While there are methodological issues apparent in our study, the results demonstrate the potential of SMSs to influence the uptake of HCT, the importance of appropriate content, and the need to determine a threshold for SMS-based interventions. These results indicate a potential for SMSs to be used more generally for interventions encouraging people to take health-related actions, and the need for further research in this field. The reasonable cost-per-tester is promising for the scale-up of such an intervention.

The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.

The Sickle Cell Disease (SCD) Ontology (SCDO, https://scdontology.h3abionet.org/) provides a comprehensive knowledge base of SCD management, systems and standardized human and machine-readable resources that unambiguously describe terminology and concepts about SCD for researchers, patients and clinicians. The SCDO was launched in 2016 and is continuously updated in quantity, as well as in quality, to effectively support the curation of SCD research, patient databasing and clinical informatics applications. SCD knowledge from the scientific literature is used to update existing SCDO terms and create new terms where necessary. Here, we report major updates to the SCDO, from December 2019 until April 2021, for promoting interoperability and facilitating SCD data harmonization, sharing and integration across different studies and for retrospective multi-site research collaborations. SCDO developers continue to collaborate with the SCD community, clinicians and researchers to improve specific ontology areas and expand standardized descriptions to conditions influencing SCD phenotypic expressions and clinical manifestations of the sickling process, e.g. thalassemias. Database URL: https://scdontology.h3abionet.org/.

Factors associated with blood pressure variation in sickle cell disease patients: a systematic review and meta-analyses.

OBJECTIVES: Blood pressure (BP) values ≥120/70 mmHg considerably increase the risk of pulmonary hypertension and renal dysfunction in Sickle Cell Disease (CSD) patients and ultimately increased morbidity and mortality. This has led to the development of the term relative systemic hypertension (RSH). RSH was defined as Systolic BP 120-139 mm Hg or diastolic BP 70-89 mm Hg, whereas systemic hypertension is defined as Systolic BP ≥ 140 mm Hg or diastolic BP ≥ 90 mm Hg. Systematic identification of BP variations and risk factors in SCD patients could promote effective management. This review aimed to identify factors associated with BP variation among SCD patients. METHODS: We searched PubMed, Scopus, Web of Science, and Google Scholar up to December 2020 with no geographical or language restrictions. Two reviewers independently screened and summarized data from eligible studies. RESULTS: Advancing age, gender, higher body weight, hemoglobin, eGFR, triglycerides, greater hematocrit, higher blood viscosity, history of blood transfusion, and targeted variants in DRD2 and MIR4301 genes were independently associated with the risk of hypertension in SCD patients. CONCLUSION: Interventions that consider these risk factors may potentially contribute to lower BP pressure in SCD patients and prevent the development of severe complications.

Skills Capacity Building For Health Care Services and Research Through the Sickle Pan African Research Consortium.

Skills development, the building of human capacity, is key to any sustainable capacity building effort, however, such undertakings require adaptable and tailored strategies. The Sickle Pan-African Research Consortium (SPARCo) is building capacity in sickle cell disease (SCD) management and research in sub-Saharan Africa, including a multi-national SCD patient registry, this is underpinned by skills development activities in data, research, and SCD management. Method: The SPARCo Skills Working Group was set up with the mandate of coordinating skills development activities across the three SPARCo sites in Ghana, Nigeria and Tanzania. To tailor activities to the requirements of the consortium, a needs assessment was conducted at the start of the project which identified skills required for SCD management and research and catalogued existing external and internal training programmes. The needs assessment highlighted differences in skill levels between the sites and different organisational structures which required tailored skills development activities at individual, site and consortium levels. Strategy: Based on the needs and the resources available, different types of training activities were implemented: these included online, blended and face to face activities. In order to create a sustainable skills development programme, existing short, medium, long-term, on-job training activities were used wherever possible. World Sickle Cell Day (19th June) was leveraged for training and health education activities. Results: SPARCo has recorded 1,726 participants in skills development activities across the three sites. Skills have been enhanced in data management, SCD and research to underpin the core deliverables of SPARCo. Conclusion and Lessons Learned: The baseline needs assessments and continual review and adjustment were critical for development of an effective skill development strategy for the consortium. This adaptability was particularly valuable during the COVID-19 pandemic. The sustainability plan leveraged existing programmes and activities and has created a pool of people with required skills for health care and research in SCD. To be effective, skills development programmes need to take into account existing capacity, training opportunities and local conditions. The model was applied to SCD and is adaptable to other skills development in healthcare and research in low and middle- income countries.

Clinical characteristics and risk factors of relative systemic hypertension and hypertension among sickle cell patients in Cameroon.

Increased blood pressure (BP) has been associated with higher risk of stroke and mortality in Sickle Cell Disease (SCD). We investigated risk factors associated with Relative Systemic Hypertension (RSH) or systemic hypertension in SCD patients in Cameroon. Using R, Multivariate multinomial logistic regression modeling was used to examine the effects of the demographic, anthropometric, clinical, and laboratory factors to determine risk factors. A total of 815 individuals with SCD, including 380 (46.6%) males were analyzed. At baseline, the median age [interquartile range] was 18.0 [12.0-25.0] years, ranging from 3 to 66 years. Approximately three-quarters of the patients (n = 645; 79.1%) had normal BP, 151 (18.5%) had RSH and 19 (2.3%) had hypertension. Age (P < 0.001) and gender (P = 0.022) were significantly different across the BP categories. Weight (P < 0.001), height (P < 0.001), BMI (P < 0.001), pulse pressure (P = 0.020), history of stroke (P = 0.012), hemoglobin level (P = 0.002), red blood cell count (P = 0.031), creatinine (P < 0.001), and (estimated glomerular filtration rate) eGFR (P = 0.002) was also significantly different across the three BP categories. After adjustment, the significantly associated factors of RSH in the SCD patients were age [OR = 1.03, (95% CI = 1.01-1.06), P < 0.010], male gender [OR = 1.54, (95% CI = 1.04-2.27), P = 0.029], BMI [OR = 1.10, (95% CI = 1.04-1.17), P = 0.001]. After adjustment, the independent variables significantly associated factors of Hypertension in the SCD patients were age [OR = 1.05, (95% CI = 1.01-1.10), P = 0.034], male gender [OR = 3.31, (95% CI = 1.04-10.52), P = 0.042], BMI [OR = 1.14, (95% CI = 1.01-1.29), P = 0.027]. Creatinine was significantly associated with RSH [OR =1.31 (1.05-1.63), P = 0.016]. SCD patients with RSH or hypertension maybe at increased risk of renal dysfunction. We found relatively high prevalence of RSH and hypertension (20.8%) in SCD patients in Cameroon. Tailored Interventions that consider major risk factors (age, gender, and BMI) may lower BP pressure and prevent severe complications.

A View on Genomic Medicine Activities in Africa: Implications for Policy.

Genomics policy development involves assessing a wide range of issues extending from specimen collection and data sharing to whether and how to utilize advanced technologies in clinical practice and public health initiatives. A survey was conducted among African scientists and stakeholders with an interest in genomic medicine, seeking to evaluate: 1) Their knowledge and understanding of the field. 2) The institutional environment and infrastructure available to them. 3) The state and awareness of the field in their country. 4) Their perception of potential barriers to implementation of precision medicine. We discuss how the information gathered in the survey could instruct the policies of African institutions seeking to implement precision, and more specifically, genomic medicine approaches in their health care systems in the following areas: 1) Prioritization of infrastructures. 2) Need for translational research. 3) Information dissemination to potential users. 4) Training programs for specialized personnel. 5) Engaging political stakeholders and the public. A checklist with key requirements to assess readiness for implementation of genomic medicine programs is provided to guide the process from scientific discovery to clinical application.

Guideline for feedback of individual genetic research findings for genomics research in Africa.

As human genomics research in Africa continues to generate large amounts of data, ethical issues arise regarding how actionable genetic information is shared with research participants. The Human Heredity and Health in Africa Consortium (H3Africa) Ethics and Community Engagement Working group acknowledged the need for such guidance, identified key issues and principles relevant to genomics research in Africa and developed a practical guideline for consideration of feeding back individual genetic results of health importance in African research projects. This included a decision flowchart, providing a logical framework to assist in decision-making and planning for human genomics research projects. Although presented in the context of the H3Africa Consortium, we believe the principles described, and the decision flowchart presented here is applicable more broadly in African genomics research.

"Black Lives Matter and Black Research Matters": the African Society of Human Genetics' call to halt racism in science.

The African Society of Human Genetics (AfSHG) was formed to provide a forum for human genetics and genomics scientists in Africa to interact, network, and collaborate. This is critical to facilitate development of solutions to the public health burden of many rare and common diseases across the continent. AfSHG fully supports the Black Lives Matter movement, which is dedicated to fighting racism and ensuring that society values the lives and humanity of Black people. The AfSHG would like to add its "voice" to the public outcry against racism sparked by George Floyd's death and to declare its commitment to ensuring that injustice and systematic racism, as well as abuse and exploitation of Africans and their biological material, are no longer tolerated. This is particularly relevant now as African genomic variation is poised to make significant contributions across several disciplines including ancestry, personalized medicine, and novel drug discovery. "Black Lives Matter and Black Research Matters" is AfSHG's call for the global community to support halting, and reversing, the perpetuation of exploitation of African people through neocolonial malpractices in genomic research. We also propose five key ways to curb racism in science, so that we can move forward together, with a common humanity, collectively embracing scientific endeavors.

Development of multi-level standards of care recommendations for sickle cell disease: Experience from SickleInAfrica.

Introduction: Sickle Cell Disease (SCD) causes significant morbidity and mortality particularly in sub-Saharan Africa (SSA) where it contributes to early childhood deaths. There is need to standardize treatment guidelines to help improve overall SCD patient health outcomes. We set out to review existing guidelines on SCD and to set minimum standards for management of SCD for the different referral levels of healthcare. Methods: A standards of care working group (SoC-WG) was established to develop the SoC recommendations. About 15 available SCD management guidelines and protocols were reviewed and themes extracted from them. The first draft was on chosen themes with 64 major headings and subtopics. Using a summarised WHO levels of referral document, we were able to get six different referral levels of healthcare. The highest referral level was the tertiary facilities whilst the lowest level was the home setting. Recommendations for SCD management for the regional, district, sub-districts, health posts and CHPs compounds were also drafted. Results: The results from this review yielded a guidelines document which had recommendations for management of SCD on 64 topics and subtopic for all the six (6) different referral levels. Discussions: Every child with SCD need to receive comprehensive care that is coordinated at each level. This recommendation is unique in terms of the availability of recommendations for different levels of care as compared to the traditional guidelines which is more focused at the tertiary levels. Patients can access care at any of the other lower referral hospitals and be managed with recommendations that are in keeping with institutional resources at that level. When such patients need care that requires expertise that is not available at that level, the recommendations will be to refer to the appropriate referral level where those expertise are available. This encourages patients to have good clinical care nearer their homes but also having access to specialist screening modalities and expertise at the tertiary hospitals if need be. With this, patient are not limited to a specific referral level when interventions cannot be instituted for them. Conclusion: This SoC recommendations document is a useful material that can be used for consistent standards of treatment in SSA.

Establishing a database for sickle cell disease patient mapping and survival tracking: The sickle pan-african research consortium Nigeria example.

Background: The Sickle Pan-African Research Consortium (SPARCO) and Sickle Africa Data Coordinating Center (SADaCC) were set up with funding from the US National Institute of Health (NIH) for physicians, scientists, patients, support groups, and statisticians to collaborate to reduce the high disease burden and alleviate the impact of Sickle Cell Disease (SCD) in Africa. For 5 years, SPARCO and SADaCC have been collecting basic clinical and demographic data from Nigeria, Tanzania, and Ghana. The resulting database will support analyses to estimate significant clinical events and provide directions for targeting interventions and assessing their impacts. Method: The Nigerian study sited at Centre of Excellence for Sickle Cell Disease Research and Training (CESRTA), University of Abuja, adopted REDCap for online database management. The case report form (CRF) was adapted from 1,400 data elements adopted by SPARCO sites. It captures 215 data elements of interest across sub-sites, i.e., demographic, social, diagnostic, clinical, laboratory, imaging, and others. These were harmonized using the SADaCC data dictionary. REDCap was installed on University of Abuja cloud server at https://www.redcap.uniabuja.edu.ng. Data collected at the sites are sent to CESRTA for collation, cleaning and uploading to the database. Results: 7,767 people living with sickle cell disease were enrolled at 25 health institutions across the six zones in Nigeria with 5,295 having had at least one follow-up visit with their clinical data updated. They range from 44 to 1,180 from 3 centers from South East, 4 from South, 5 from South West, 8 from North Central, 4 in North West and 3 in the North East. North West has registered 1,383 patients, representing 17.8%; North East, 359 (4.6%); North Central, 2,947 (37.9%); South West, 1,609 (20.7%); South, 442 (5.7%) and South East, 1,027 patients (13.2%). Conclusion: The database is being used to support studies including analysis of clinical phenotypes of SCD in Nigeria, and evaluation of Hydroxyurea use in SCD. Reports undergoing review in journals have relied on the ease of data access in REDCap. The database is regularly updated by batch and individual record uploads while we are utilizing REDCap's in-built functions to generate simple statistic.