Data Resource Profile: Cardiovascular H3Africa Innovation Resource (CHAIR)

Post-surgery survival and associated factors for cardiac patients in Ethiopia: applications of machine learning, semi-parametric and parametric modelling

INTRODUCTION

Living in poverty, especially in low-income countries, are more affected by cardiovascular disease. Unlike the developed countries, it remains a significant cause of preventable heart disease in the Sub-Saharan region, including Ethiopia. According to the Ethiopian Ministry of Health statement, around 40,000 cardiac patients have been waiting for surgery in Ethiopia since September 2020. There is insufficient information about long-term cardiac patients' post-survival after cardiac surgery in Ethiopia. Therefore, the main objective of the current study was to determine the long-term post-cardiac surgery patients' survival status in Ethiopia.

METHODS

All patients attended from 2012 to 2023 throughout the country were included in the current study. The total number of participants was 1520 heart disease patients. The data collection procedure was conducted from February 2022- January 2023. Machine learning algorithms were applied. Gompertz regression was used also for the multivariable analysis report.

RESULTS

From possible machine learning models, random survival forest were preferred. It emphasizes, the most important variable for clinical prediction was SPO2, Age, time to surgery waiting time, and creatinine value and it accounts, 42.55%, 25.17%,11.82%, and 12.19% respectively. From the Gompertz regression, lower saturated oxygen, higher age, lower ejection fraction, short period of cardiac center stays after surgery, prolonged waiting time to surgery, and creating value were statistically significant predictors of death outcome for post-cardiac surgery patients' survival in Ethiopia.

CONCLUSION

Some of the risk factors for the death of post-cardiac surgery patients are identified in the current investigation. Particular attention should be given to patients with prolonged waiting times and aged patients. Since there were only two fully active cardiac centers in Ethiopia it is far from an adequate number of centers for more than 120 million population, therefore, the study highly recommended to increase the number of cardiac centers that serve as cardiac surgery in Ethiopia.

Factors associated with frequency of fruit and vegetable consumption among selected sub-Saharan African populations: evidence from the Cardiovascular H3Africa Innovation Resource Project

BACKGROUND

Frequent fruit and vegetable consumption is considered a promising dietary behaviour that protects health. However, most existing studies about the factors associated with this phenomenon among Africans are based on single-country reports, apart from one meta-regression combining smaller studies. This study harmonized large datasets and assessed factors associated with the frequency of fruit and vegetable consumption in this population.

METHODS

Individual-level data on sociodemographics, lifestyle and diet from 20 443 participants across five African countries (Burkina Faso, Ghana, Kenya, South Africa and Nigeria), from the Stroke Investigative Research and Educational Network (SIREN) and Africa Wits-INDEPTH partnership for Genomic Research (AWI-Gen) studies, were harmonized. Total frequency of fruit and vegetable consumption (in portions/week) was classified as 'low' (≤6), 'moderate' (7-14) and 'high' (≥15). Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) of factors associated with the total frequency of fruit and vegetable consumption (using 'low' consumption as the reference) were estimated using multinomial regression models.

RESULTS

Mean age of participants was 54.3 ± 11.8 years, 10 641 (52.1%) were female, and the median (interquartile range) frequency of total fruit and vegetable consumption was 10.0 (4.0, 21.0) portions/week. Participants with a family history of cardiovascular disease [moderate (aOR, 0.92; 95% CI, 0.85, 1.00) and high (aOR, 0.85; 95% CI, 0.78, 0.92)], current smokers [moderate (aOR, 0.83; 95% CI, 0.74, 0.94) and high (aOR, 0.78; 95% CI, 0.69, 0.88)], current alcohol users [moderate (aOR, 0.92; 95% CI, 0.85, 1.00) and high (aOR, 0.82; 95% CI, 0.76, 0.89)] and physically inactive participants [moderate (aOR, 0.85; 95% CI, 0.75, 0.96) and high (aOR, 0.80; 95% CI, 0.70, 0.90)] were less likely to consume fruits and vegetables frequently.

CONCLUSION

Africans with lifestyle risk factors for cardiovascular disease were less likely to consume fruit and vegetables frequently.

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.

Human height: a model common complex trait

CONTEXT

Like other complex phenotypes, human height reflects a combination of environmental and genetic factors, but is notable for being exceptionally easy to measure. Height has therefore been commonly used to make observations later generalised to other phenotypes though the appropriateness of such generalisations is not always considered.

OBJECTIVES

We aimed to assess height's suitability as a model for other complex phenotypes and review recent advances in height genetics with regard to their implications for complex phenotypes more broadly.

METHODS

We conducted a comprehensive literature search in PubMed and Google Scholar for articles relevant to the genetics of height and its comparatibility to other phenotypes.

RESULTS

Height is broadly similar to other phenotypes apart from its high heritability and ease of measurment. Recent genome-wide association studies (GWAS) have identified over 12,000 independent signals associated with height and saturated height's common single nucleotide polymorphism based heritability of height within a subset of the genome in individuals similar to European reference populations.

CONCLUSIONS

Given the similarity of height to other complex traits, the saturation of GWAS's ability to discover additional height-associated variants signals potential limitations to the omnigenic model of complex-phenotype inheritance, indicating the likely future power of polygenic scores and risk scores, and highlights the increasing need for large-scale variant-to-gene mapping efforts.

Frequent vegetable consumption is inversely associated with hypertension among indigenous Africans

AIMS

The relationship between vegetable consumption and hypertension occurrence remains poorly characterized in sub-Saharan Africa. This study assessed the association of vegetable consumption with odds of hypertension among indigenous Africans.

METHODS AND RESULTS

We harmonized data on prior vegetable consumption and hypertension occurrence (defined as one of the following conditions; systolic blood pressure ≥140 or diastolic blood pressure ≥90 mmHg or previous diagnosis or use of antihypertensive medications) from 16 445 participants across five African countries (Nigeria, South Africa, Kenya, Ghana and Burkina Faso) in the Stroke Investigative Research and Educational Network and Africa Wits-INDEPTH partnership for Genomic studies. Vegetable consumption (in servings/week) was classified as 'low' (<6). 'moderate' (6-11), 'sufficient' (12-29), and 'high' (≥30). Odds ratios (ORs) and 95% confidence interval (CI) of hypertension were estimated by categories of vegetable consumption (using 'low' consumption as reference), adjusting for sex, age in years, family history of cardiovascular diseases, education, smoking, alcohol use, physical inactivity, body mass index, diabetes mellitus and dyslipidaemia using logistic regressions at P < 0.05. The mean age of participants was 53.0 ( ± 10.7) years, and 7552 (45.9%) were males, whereas 7070 (42.9%) had hypertension. In addition, 6672(40.6%) participants had 'low' vegetable consumption, and 1758(10.7%) had 'high' vegetable consumption. Multivariable-adjusted OR for hypertension by distribution of vegetable consumption (using 'low' consumption as reference) were 1.03 (95% CI: 0.95, 1.12) for 'moderate' consumption; 0.80 (0.73, 0.88) for 'sufficient', and 0.81 (0.72, 0.92) for 'high' consumption, P-for-trend <0.0001.

CONCLUSION

Indigenous Africans who consumed at least 12 servings of vegetables per week were less likely to be found hypertensive, particularly among males and young adults.

Genomics in Egypt: Current Status and Future Aspects

Egypt is the third most densely inhabited African country. Due to the economic burden and healthcare costs of overpopulation, genomic and genetic testing is a huge challenge. However, in the era of precision medicine, Egypt is taking a shift in approach from “one-size-fits all” to more personalized healthcare via advancing the practice of medical genetics and genomics across the country. This shift necessitates concrete knowledge of the Egyptian genome and related diseases to direct effective preventive, diagnostic and counseling services of prevalent genetic diseases in Egypt. Understanding disease molecular mechanisms will enhance the capacity for personalized interventions. From this perspective, we highlight research efforts and available services for rare genetic diseases, communicable diseases including the coronavirus 2019 disease (COVID19), and cancer. The current state of genetic services in Egypt including availability and access to genetic services is described. Drivers for applying genomics in Egypt are illustrated with a SWOT analysis of the current genetic/genomic services. Barriers to genetic service development in Egypt, whether economic, geographic, cultural or educational are discussed as well. The sensitive topic of communicating genomic results and its ethical considerations is also tackled. To understand disease pathogenesis, much can be gained through the advancement and integration of genomic technologies via clinical applications and research efforts in Egypt. Three main pillars of multidisciplinary collaboration for advancing genomics in Egypt are envisaged: resources, infrastructure and training. Finally, we highlight the recent national plan to establish a genome center that will aim to prepare a map of the Egyptian human genome to discover and accurately determine the genetic characteristics of various diseases. The Reference Genome Project for Egyptians and Ancient Egyptians will initialize a new genomics era in Egypt. We propose a multidisciplinary governance system in Egypt to support genomic medicine research efforts and integrate into the healthcare system whilst ensuring ethical conduct of data.

African Global Representation in Biomedical Sciences

African populations are diverse in their ethnicity, language, culture, and genetics. Although plagued by high disease burdens, until recently the continent has largely been excluded from biomedical studies. Along with limitations in research and clinical infrastructure, human capacity, and funding, this omission has resulted in an underrepresentation of African data and disadvantaged African scientists. This review interrogates the relative abundance of biomedical data from Africa, primarily in genomics and other omics. The visibility of African science through publications is also discussed. A challenge encountered in this review is the relative lack of annotation of data on their geographical or population origin, with African countries represented as a single group. In addition to the abovementioned limitations,the global representation of African data may also be attributed to the hesitation to deposit data in public repositories. Whatever the reason, the disparity should be addressed, as African data have enormous value for scientists in Africa and globally.

African genetic diversity and adaptation inform a precision medicine agenda

The deep evolutionary history of African populations, since the emergence of modern humans more than 300,000 years ago, has resulted in high genetic diversity and considerable population structure. Selected genetic variants have increased in frequency due to environmental adaptation, but recent exposures to novel pathogens and changes in lifestyle render some of them with properties leading to present health liabilities. The unique discoverability potential from African genomic studies promises invaluable contributions to understanding the genomic and molecular basis of health and disease. Globally, African populations are understudied, and precision medicine approaches are largely based on data from European and Asian-ancestry populations, which limits the transferability of findings to the continent of Africa. Africa needs innovative precision medicine solutions based on African data that use knowledge and implementation strategies aligned to its climatic, cultural, economic and genomic diversity.

Non-communicable diseases pandemic and precision medicine: Is Africa ready?

Non-communicable diseases (NCDs) kill more than 41 million people every year, accounting for 71% of all deaths globally. The prevalence of NCDs is estimated to be higher than that of infectious diseases in Africa by 2030. Precision medicine may help with early identification of cases, resulting in timely prevention and improvement in the efficacy of treatments. However, Africa has been lagging behind in genetic research, a key component of the precision medicine initiative. A number of genomic research initiatives which could lead to translational genomics are emerging on the African continent which includes the Non-communicable Diseases Genetic Heritage Study (NCDGHS) and the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network. These offer a promise that precision medicine can be applied in African countries. This review evaluates the advances of genetic studies for cancer, hypertension, type 2 diabetes and body mass index (BMI) in Africa.

The Egyptian Collaborative Cardiac Genomics (ECCO-GEN) Project: defining a healthy volunteer cohort

The integration of comprehensive genomic and phenotypic data from diverse ethnic populations offers unprecedented opportunities toward advancements in precision medicine and novel diagnostic technologies. Current reference genomic databases are not representative of the global human population, making variant interpretation challenging, especially in underrepresented populations, such as the North African population. To address this, the Egyptian Collaborative Cardiac Genomics (ECCO-GEN) Project launched a study comprising 1000 individuals free of cardiovascular disease (CVD). Here, we present the first 391 Egyptian healthy volunteers recruited to establish a pilot phenotyped control cohort. All individuals underwent detailed clinical investigation, including cardiac magnetic resonance imaging (MRI), and were sequenced using a targeted panel of 174 genes with reported roles in inherited cardiac conditions. We identified 1262 variants in 27 cardiomyopathy genes of which 15.1% were not captured in current global and regional genetic reference databases (here: gnomAD and Great Middle Eastern Variome). The ECCO-GEN project aims at defining the genetic landscape of an understudied population and providing individual-level genetic and phenotypic data to support future studies in CVD and population genetics.

Determinants of Selected Cardiovascular Diseases among Adult Patients at Cardiac Clinic of Debre Berhan Referral Hospital, Ethiopia: Unmatched Case-Control Study

Background

Africans are experiencing a rapid epidemiological transition characterized by urbanization and lifestyle changes, which are thought to contribute to increased incidence and prevalence of cardiovascular diseases (CVDs) in many African countries, including Ethiopia. Despite this, however, there is scarcity of evidence on cardiovascular disease risk factors among adults in the current research setting. This study thus aimed at assessing determinants of selected cardiovascular diseases among adult patients at Debre Berhan Referral Hospital (DBRH). Methodology. An unmatched case-control study was conducted on 143 newly diagnosed patients with CVDs and 286 controls at the cardiac clinic of DBRH from June to September 2017. Primary data were collected using the WHO-STEPS wise structured questionnaires. Multiple logistic regression analysis was used to identify potential risk factors for cardiovascular diseases at p values < 0.05.

Result

The mean age of study participants is estimated as 45.5 ± 13.8 and ranges from 25 to 64 years. Sixty-one (42.7%) of cases and 147 (51.4%) of controls are males. Half of the cases (49.9%) had ischemic heart diseases (IHD), and 44.1% of cases had hypertensive heart disease (HHD), whereas the rest had chronic valvular heart disease (CRVHD) (4.2%) and peripheral and vascular disease (2.1%). This study identified older age as a risk factor for CVD: age group 35–44 years (adjusted odds ratio (AOR) = 2.20; 95% CI: 1.05–4.62), 45-54 years (AOR = 4.23; 95% CI: 2.19–8.16), and 55-64 years (AOR = 5.98; 95% CI: 3.26–10.98). Other risk factors were smoking history (AOR = 9.52; 95% CI: 2.12–42.8), low level of physical activity (AOR = 2.19; 95% CI: 1.10–5.02), and higher waist circumference (AOR = 2.75; 95% CI: 1.16–6.56).

Conclusion

This study has demonstrated that the most frequent risk factors for CVD were older age, cigarette smoking, physical inactivity, and abdominal obesity. Therefore, behavior change communication focusing on lifestyle modification including regular physical activities, smoking cessation, and a balanced diet should be strengthened.

Regional Patterns and Association Between Obesity and Hypertension in Africa: Evidence From the H3Africa CHAIR Study

Hypertension and obesity are the most important modifiable risk factors for cardiovascular diseases, but their association is not well characterized in Africa. We investigated regional patterns and association of obesity with hypertension among 30 044 continental Africans. We harmonized data on hypertension (defined as previous diagnosis/use of antihypertensive drugs or blood pressure [BP]≥140/90 mmHg/BP≥130/80 mmHg) and obesity from 30 044 individuals in the Cardiovascular H3Africa Innovation Resource across 13 African countries. We analyzed data from population-based controls and the Entire Harmonized Dataset. Age-adjusted and crude proportions of hypertension were compared regionally, across sex, and between hypertension definitions. Logit generalized estimating equation was used to determine the independent association of obesity with hypertension (P value <5%). Participants were 56% women; with mean age 48.5±12.0 years. Crude proportions of hypertension (at BP≥140/90 mmHg) were 47.9% (95% CI, 47.4-48.5) for Entire Harmonized Dataset and 42.0% (41.1-42.7) for population-based controls and were significantly higher for the 130/80 mm Hg threshold at 59.3% (58.7-59.9) in population-based controls. The age-adjusted proportion of hypertension at BP≥140/90 mmHg was the highest among men (33.8% [32.1-35.6]), in western Africa (34.7% [33.3-36.2]), and in obese individuals (43.6%; 40.3-47.2). Obesity was independently associated with hypertension in population-based controls (adjusted odds ratio, 2.5 [2.3-2.7]) and odds of hypertension in obesity increased with increasing age from 2.0 (1.7-2.3) in younger age to 8.8 (7.4-10.3) in older age. Hypertension is common across multiple countries in Africa with 11.9% to 51.7% having BP≥140/90 mmHg and 39.5% to 69.4% with BP≥130/80 mmHg. Obese Africans were more than twice as likely to be hypertensive and the odds increased with increasing age.

Evaluating the promise of inclusion of African ancestry populations in genomics

The lack of representation of diverse ancestral backgrounds in genomic research is well-known, and the resultant scientific and ethical limitations are becoming increasingly appreciated. The paucity of data on individuals with African ancestry is especially noteworthy as Africa is the birthplace of modern humans and harbors the greatest genetic diversity. It is expected that greater representation of those with African ancestry in genomic research will bring novel insights into human biology, and lead to improvements in clinical care and improved understanding of health disparities. Now that major efforts have been undertaken to address this failing, is there evidence of these anticipated advances? Here, we evaluate the promise of including diverse individuals in genomic research in the context of recent literature on individuals of African ancestry. In addition, we discuss progress and achievements on related technological challenges and diversity among scientists conducting genomic research.