Whole-genome sequencing across 449 samples spanning 47 ethnolinguistic groups provides insights into genetic diversity in Nigeria

African populations have been drastically underrepresented in genomics research, and failure to capture the genetic diversity across the numerous ethnolinguistic groups (ELGs) found on the continent has hindered the equity of precision medicine initiatives globally. Here, we describe the whole-genome sequencing of 449 Nigerian individuals across 47 unique self-reported ELGs. Population structure analysis reveals genetic differentiation among our ELGs, consistent with previous findings. From the 36 million SNPs and insertions or deletions (indels) discovered in our dataset, we provide a high-level catalog of both novel and medically relevant variation present across the ELGs. These results emphasize the value of this resource for genomics research, with added granularity by representing multiple ELGs from Nigeria. Our results also underscore the potential of using these cohorts with larger sample sizes to improve our understanding of human ancestry and health in Africa.

Spatial distribution and ecological niche modeling of geographical spread of Anopheles gambiae complex in Nigeria using real time data

The need for evidence-based data, to inform policy decisions on malaria vector control interventions in Nigeria, necessitated the establishment of mosquito surveillance sites in a few States in Nigeria. In order to make evidence-based-decisions, predictive studies using available data becomes imperative. We therefore predict the distribution of the major members of the Anopheles gambiae s.l. in Nigeria. Immature stages of Anopheles were collected from 72 study locations which span throughout the year 2020 resulted in the identification of over 60,000 Anopheline mosquitoes. Of these, 716 breeding sites were identified with the presence of one or more vector species from the An. gambiae complex and were subsequently used for modelling the potential geographical distribution of these important malaria vectors. Maximum Entropy (MaxEnt) distribution modeling was used to predict their potentially suitable vector habitats across Nigeria. A total of 23 environmental variables (19 bioclimatic and four topographic) were used in the model resulting in maps of the potential geographical distribution of three dominant vector species under current climatic conditions. Members of the An. gambiae complex dominated the collections (98%) with Anopheles stephensi, Anopheles coustani, Anopheles funestus, Anopheles moucheti, Anopheles nilli also present. An almost equal distribution of the two efficient vectors of malaria, An. gambiae and Anopheles coluzzii, were observed across the 12 states included in the survey. Anopheles gambiae and Anopheles coluzzii had almost equal, well distributed habitat suitability patterns with the latter having a slight range expansion. However, the central part of Nigeria (Abuja) and some highly elevated areas (Jos) in the savannah appear not suitable for the proliferation of these species. The most suitable habitat for Anopheles arabiensis was mainly in the South-west and North-east. The results of this study provide a baseline allowing decision makers to monitor the distribution of these species and establish a management plan for future national mosquito surveillance and control programs in Nigeria.

Health-related quality of life among children/adolescents living with HIV/AIDS in Lagos State, Nigeria

Health-Related Quality of Life (HRQL) is commonly used to assess the impact of health status on quality of life. The HRQL data obtained does not follow the assumption of normality and a non-parametric test was used to make inference in this study. This study compares the characteristics of children with HRQL classified as good, intermediate, and poor quality of life. The children and adolescents that have a good health-related quality of life had a mean rank of 75.5, intermediate, 27.0 while children and adolescents with poor HRQL had a mean rank of 8.5. The health -related quality of life differs significantly across the demographic characteristics. However, tertiary education does not differ significantly on HRQL. The Kruskal-Wallis's chi-squared was 76.95 with two degrees of freedom and p-value < 2.2e-16. The p-value < 0.05 indicates sufficient evidence that HRQL of children and adolescents differs significantly across the three categories. Conclusively, children and adolescents in the three categories have different quality of life. It is clear that most of the children and adolescents had a good health-related quality of life once they have been taking their drugs regularly as prescribed by the physician.

A multi-centre observational study of HIV, tuberculosis and risk of chronic lung disease in urban West Africa

OBJECTIVE

HIV and tuberculosis (TB) are risk factors for non-communicable chronic lung disease (CLD). Despite the high prevalence of these infections in West Africa, there are no studies that compare CLD between people with HIV and HIV-negative populations in this setting. This study sought to quantify the contribution of HIV and TB infection in addition to conventional CLD risk factors, such as tobacco and biofuel exposure, to CLD in urban West Africa.

DESIGN

A multi-centre cross-sectional study was conducted in three community clinics in Lagos, Nigeria between 2018 and 2019.

METHODS

Spirometry, questionnaires and clinical records were used to estimate prevalence of CLD and association with risk factors.

RESULTS

In total, 148 HIV-negative individuals and 170 HIV-positive individuals completed the study. Current cigarette (11 of 318, 3.5%) and lifetime domestic biofuel (6 of 318, 1.8%) exposures were low. Airway obstruction (33 of 170, 19.4% vs. 12 of 148, 8.1%, P  = 0.004) and CLD (73 of 170, 42.9% vs. 34 of 148, 23%, P  < 0.0001) were more prevalent in people with HIV compared with the HIV-negative group. HIV infection [odds ratio 2.35 (1.33, 4.17), P  = 0.003] and history of TB [odds ratio 2.09 (1.04, 4.20), P  = 0.038] were independently associated with increased risk of CLD.

CONCLUSION

HIV and TB far outweigh conventional risk factors, including tobacco and domestic biofuel exposure, as drivers of non-communicable CLD in urban West Africa. Current global policy for CLD may have limited impact on CLD in this setting. Enhanced prevention, diagnosis and management strategies for incident HIV and TB infections are likely to have a significant impact on long-term lung health in sub-Saharan Africa.

Perceptions and opinions of Nigerians to the management and response to COVID-19 in Nigeria

INTRODUCTION

we present a qualitative analysis of opinions of the Nigerian general public as to how successful healthcare strategies have been in containing the COVID-19 outbreak.

METHODS

an online qualitative survey was conducted, consisting of 30 semi-structured questions.

RESULTS

four hundred and ninety-five (495) respondents participated, ranging in age from 18 to 59 years. Over 40% of all respondents were critical of public health information. Participants saw provision of social support measures (n = 83), lack of economic, financial and social support (n = 65), enforcement of restrictions on movement outside the home, availability of face-masks and social distancing (n = 53) and provision of COVID-19 testing (n = 48) as the major things that were handled poorly by the government and health authorities.

CONCLUSION

we advocate coordinated forward planning for public safety until vaccines are widely available; while social distancing should continue. Policymakers need to be adaptable to changing conditions, given fluctuating case numbers and fatality rates.

The use of DIY (Do it yourself) sampling and telemonitoring model for COVID-19 qPCR testing scale up

The first case of COVID-19 in Nigeria was recorded on February 27, 2020, being an imported case by an Italian expatriate, to the country. Since then, there has been steady increase in the number of cases. However, the number of cases in Nigeria is low in comparison to cases reported by other countries with similar large populations, despite the poor health system prevailing in the country. This has been mainly attributed to the low testing capacity in Nigeria among other factors. Therefore, there is a need for innovative ways to increase the number of persons testing for COVID-19. The aim of the study was to pilot a nasopharyngeal swab self-sample collection model that would help increase COVID-19 testing while ensuring minimal person-to-person contact being experienced at the testing center. 216 participants took part in this study which was carried out at the Nigerian Institute of Medical Research between June and July 2020. Amongst the 216 participants, 174 tested negatives for both self-collected samples and samples collected by Professionals, 30 tested positive for both arms, with discrepancies occurring in 6 samples where the self-collected samples were positive while the ones collected by the professionals were negative. The same occurred in another set of 6 samples with the self-collected samples being negative and the professional-collected sample coming out positive, with a sensitivity of 83.3% and a specificity of 96.7%. The results of the interrater analysis are Kappa = 0.800 (95% CI, 0.690 to 0.910) which implies an outstanding agreement between the two COVID-19 sampling methods. Furthermore, since p< 0.001 Kappa (k) coefficient is statistically different from zero, our findings have shown that self-collected samples can be reliable in the diagnosis of COVID-19.

Prevalence and Presentation of Paediatric Coronavirus Disease 2019 in Lagos, Nigeria

BACKGROUND

The objective of this study was to describe the prevalence and clinical features of coronavirus disease 2019 (COVID-19) among children (≤18 years) evaluated for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection at a testing centre in Lagos, Nigeria. Methodology. This was a retrospective study. Data on the sociodemographic, clinical characteristics and SARS-CoV-2 results of participants at a modified drive-through centre for COVID-19 test sample collection over four months were retrieved from the electronic medical records (EMR). Data obtained were analyzed using SPSS version 22.0.

RESULTS

A total of 307 children (≤18 years) were evaluated in this review. The prevalence of SARS-CoV-2 infection among the paediatric population was 16.3%. The median age (interquartile range (IQR)) was 9 (4-14) years. Common symptoms reported by the positive cases were fever (40.0%), cough (32.9%), sore throat (17.1%), and runny nose (15.7%). The majority of the positive cases had mild symptoms. Fever and sore throat were associated with the positive cases.

CONCLUSION

Fever and sore throat were associated with SARS-CoV-2 infection among our cohort which buttresses the need for a high level of suspicion and clinical acumen in the management of common febrile diseases in paediatric settings.

Discovery and fine-mapping of height loci via high-density imputation of GWASs in individuals of African ancestry

Although many loci have been associated with height in European ancestry populations, very few have been identified in African ancestry individuals. Furthermore, many of the known loci have yet to be generalized to and fine-mapped within a large-scale African ancestry sample. We performed sex-combined and sex-stratified meta-analyses in up to 52,764 individuals with height and genome-wide genotyping data from the African Ancestry Anthropometry Genetics Consortium (AAAGC). We additionally combined our African ancestry meta-analysis results with published European genome-wide association study (GWAS) data. In the African ancestry analyses, we identified three novel loci (SLC4A3, NCOA2, ECD/FAM149B1) in sex-combined results and two loci (CRB1, KLF6) in women only. In the African plus European sex-combined GWAS, we identified an additional three novel loci (RCCD1, G6PC3, CEP95) which were equally driven by AAAGC and European results. Among 39 genome-wide significant signals at known loci, conditioning index SNPs from European studies identified 20 secondary signals. Two of the 20 new secondary signals and none of the 8 novel loci had minor allele frequencies (MAF) < 5%. Of 802 known European height signals, 643 displayed directionally consistent associations with height, of which 205 were nominally significant (p < 0.05) in the African ancestry sex-combined sample. Furthermore, 148 of 241 loci contained ≤20 variants in the credible sets that jointly account for 99% of the posterior probability of driving the associations. In summary, trans-ethnic meta-analyses revealed novel signals and further improved fine-mapping of putative causal variants in loci shared between African and European ancestry populations.

Improving the Understanding of the Immunopathogenesis of Lymphopenia as a Correlate of SARS-CoV-2 Infection Risk and Disease Progression in African Patients: Protocol for a Cross-sectional Study

BACKGROUND

The COVID-19 pandemic, caused by SARS-CoV-2, continues to impact health systems throughout the world with serious medical challenges being imposed on many African countries like Nigeria. Although emerging studies have identified lymphopenia as a driver of cytokine storm, disease progression, and poor outcomes in infected patients, its immunopathogenesis, as well as environmental and genetic determinants, remain unclear. Understanding the interplay of these determinants in the context of lymphopenia and COVID-19 complications in patients in Africa may help with risk stratification and appropriate deployment of targeted treatment regimens with repurposed drugs to improve prognosis.

OBJECTIVE

This study is designed to investigate the role of vitamin D status, vasculopathy, apoptotic pathways, and vitamin D receptor (VDR) gene polymorphisms in the immunopathogenesis of lymphopenia among African people infected with SARS-CoV-2.

METHODS

This cross-sectional study will enroll 230 participants, categorized as "SARS-CoV-2 negative" (n=69), "COVID-19 mild" (n=32), "hospitalized" (n=92), and "recovered" (n=37), from two health facilities in Lagos, Nigeria. Sociodemographic data, travel history, and information on comorbidities will be obtained from case files and through a pretested, interview-based structured questionnaire. Venous blood samples (5 mL) collected between 8 AM and 10 AM and aliquoted into EDTA (ethylenediaminetetraacetic acid) and plain tubes will be used for complete blood count and CD4 T cell assays to determine lymphopenia (lymphocyte count <1000 cells/µL) and CD4 T lymphocyte levels, as well as to measure the concentrations of vitamin D, caspase 3, soluble vascular cell adhesion molecule-1 (sVCAM-1), and soluble Fas ligand (sFasL) using an autoanalyzer, flow cytometry, and ELISA (enzyme-linked immunosorbent assay) techniques. Genomic DNA will be extracted from the buffy coat and used as a template for the amplification of apoptosis-related genes (Bax, Bcl-2, BCL2L12) by polymerase chain reaction (PCR) and genotyping of VDR (Apa1, Fok1, and Bsm1) gene polymorphisms by the PCR restriction fragment length polymorphism method and capillary sequencing. Total RNA will also be extracted, reverse transcribed, and subsequently quantitated by reverse transcription PCR (RT-PCR) to monitor the expression of apoptosis genes in the four participant categories. Data analyses, which include a test of association between VDR gene polymorphisms and study outcomes (lymphopenia and hypovitaminosis D prevalence, mild/moderate and severe infections) will be performed using the R statistical software. Hardy-Weinberg equilibrium and linkage disequilibrium analyses for the alleles, genotypes, and haplotypes of the genotyped VDR gene will also be carried out.

RESULTS

A total of 45 participants comprising 37 SARS-CoV-2-negative and 8 COVID-19-recovered individuals have been enrolled so far. Their complete blood counts and CD4 T lymphocyte counts have been determined, and their serum samples and genomic DNA and RNA samples have been extracted and stored at -20 °C until further analyses. Other expected outcomes include the prevalence and distribution of lymphopenia and hypovitaminosis D in the control (SARS-CoV-2 negative), confirmed, hospitalized, and recovered SARS-CoV-2-positive participants; association of lymphopenia with CD4 T lymphocyte level, serum vitamin D, sVCAM-1, sFasL, and caspase 3 levels in hospitalized patients with COVID-19; expression levels of apoptosis-related genes among hospitalized participants with COVID-19, and those with lymphopenia compared to those without lymphopenia; and frequency distribution of the alleles, genotypes, and haplotypes of VDR gene polymorphisms in COVID-19-infected participants.

CONCLUSIONS

This study will aid in the genotypic and phenotypic stratification of COVID-19-infected patients in Nigeria with and without lymphopenia to enable biomarker discovery and pave the way for the appropriate and timely deployment of patient-centered treatments to improve prognosis.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/21242.

Predictors and prognoses of new onset post-stroke anxiety at one year in black Africans

BACKGROUND

There is relatively limited information on the risk factors and outcome of new onset Poststroke Anxiety (PSA) in Low- and Middle-Income Countries. We estimated incidence, cumulative incidence, risk factors and outcome of new onset anxiety in the first year of stroke among African stroke survivors.

METHODS

We analyzed the dataset of a completed clinical trial comprising patients enrolled to test an intervention designed to improve one-year blood pressure control among recent (≤ one month) stroke survivors in Nigeria. Anxiety was measured using the Hospital Anxiety and Depression Scale. Outcomes were assessed using the modified Rankin Scale (mRS), Community screening instrument for dementia (CSID) and Health Related Quality of Life in Stroke Patients (HRQOLISP-26).

RESULTS

Among 322 stroke survivors who were free of anxiety at baseline, we found a one-year cumulative incidence of 34% (95% CI = 28.6-39.3). Rates were 36.2% (95% CI =29.6-42.7) for men and 29.2% (95% CI =19.9-38.3) for women. In multivariate Cox regression analyses, haemorrhagic stroke type was associated with higher risk of new onset PSA (Hazard Ratio=1.52, 95% CI =1.01-2.29). New onset PSA was independently associated with cognitive [(mean difference (MD) in CSID scores=1.1, 95% C.I=0.2, 1.9)] and motor decline (MD in mRS scores= -0.2, 95% C.I= -0.4, -0.02), as well as poorer quality of life overtime (MD in total HRQOLISP-26 scores=3.6, 95% C.I=1.0, 6.2).

CONCLUSION

One in 3 stroke survivors in Nigeria had PSA at one year. Clinicians in SSA should pay special attention to survivors of haemorrhagic stroke as they are at higher risk of incident anxiety and therefore its consequences.

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.

Upheaval in cancer care during the COVID-19 outbreak

On Monday, 23 March 2020, Nigeria recorded its first mortality from the novel global COVID-19 outbreak. Before this, the country reported 36 confirmed cases (at the time of writing) and has discharged home two cases after weeks of care at a government-approved isolation centre in Lagos State. This first mortality was that of a 67-year-old man with a history of multiple myeloma, a type of blood cancer. He was undergoing chemotherapy and had just returned to Nigeria following medical treatment in the United Kingdom. The novel COVID-19 pandemic has grounded several global activities including the provision of health care services to people with chronic conditions such as cancer. Evidence from China suggests that cancer patients with COVID-19 infection are a vulnerable group, with a higher risk of severe illness resulting in intensive care unit admissions or death, particularly if they received chemotherapy or surgery. This letter is an attempt to suggest practicable interventions such as the use of existing digital health platforms to limit patients' and oncology professionals' physical interactions as a way of reducing the risk of COVID-19 infection transmission amongst cancer patients and oncologists, as well as outlining effective strategies to ensure that cancer care is not completely disrupted during the outbreak.

Acute kidney injury among adult patients undergoing major surgery in a tertiary hospital in Nigeria

Background

Acute kidney injury (AKI) is an underreported but major cause of morbidity and mortality among patients undergoing major surgical interventions in sub-Saharan Africa (SSA). Whereas AKI is often seen following major cardiac surgery in high-income countries, a similar spectrum of surgical diseases and interventions is not seen in developing countries. The impacts on surgical outcomes have also not been well characterized in SSA. This study aimed at identifying risk factors, incidence and determinants and short-term outcomes of AKI among patients undergoing major surgery.

Methods

This was a cohort study of adult patients undergoing major surgery at the University College Hospital, Ibadan, Nigeria. Data obtained were sociodemographic details, risk factors for AKI, details of surgery, anaesthesia and intra-operative events and short-term outcomes. Blood samples were obtained for pre-operative (pre-op) full blood count, serum electrolytes, blood urea and creatinine (SCr). Post-operatively (Post-op) SCr was determined at 24 h, Day 7 post-op and weekly until each patient was discharged.

Results

A total of 219 subjects who had major surgery (86.3% elective) were enrolled. The median age of the patients was 46 (range 18-73) years and 72.6% were females. The surgeries performed were mostly simple mastectomies (37.4%), exploratory laparotomies (22.8%) and total thyroidectomies (16.4%). The incidences of AKI were 18.7% at 24 h and 17.4% at Day 7 post-op, while cumulative AKI incidence was 22.5% at 1-week post-op. Pre-op elevated SCr [odds ratio (OR) 3.86], sepsis (OR 2.69), anaemia (OR 2.91) and duration of surgery >120 min (OR 1.75) were independently associated with AKI. In-patient mortality was 20.4% in individuals with AKI and 5.3% in those without AKI (P < 0.01).

Conclusion

Peri-operative risk factors for AKI are common among patients undergoing major surgery in SSA hospitals. The cumulative incidence of AKI was high and independently associated with pre-op sepsis, anaemia, pre-existing kidney dysfunction and duration of surgery >120 min.

Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium

Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHR_adjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHR_adjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHR_adjBMI and eight previously established loci at P < 5×10⁻⁸: seven for BMI, and one for WHR_adjBMI in African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHR_adjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHR_adjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (<5%). In the trans-ethnic fine mapping of 47 BMI loci and 27 WHR_adjBMI loci that were locus-wide significant (P < 0.05 adjusted for effective number of variants per locus) from the African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHR_adjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHR_adjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations.

Genome-wide association studies (GWAS) have identified >300 genetic regions that influence body size and shape as measured by body mass index (BMI) and waist-to-hip ratio (WHR), respectively, but few have been identified in populations of African ancestry. We conducted large scale high coverage GWAS and replication of these traits in 52,895 and 23,095 individuals of African ancestry, respectively, followed by additional replication in European populations. We identified 10 genome-wide significant loci in all individuals, and an additional seven loci by analyzing men and women separately. We combined African and European ancestry GWAS and were able to narrow down 43 out of 74 African ancestry associated genetic regions to contain small number of putative causal variants. Our results highlight the improvement of applying high density genome coverage and combining multiple ancestries in the identification and refinement of location of genetic regions associated with adiposity traits.

Directional dominance on stature and cognition in diverse human populations

Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10(-300), 2.1 × 10(-6), 2.5 × 10(-10) and 1.8 × 10(-10), respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months' less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

Comparison of patients from Nigeria and the USA highlights modifiable risk factors for sickle cell anemia complications

To identify factors that affect manifestations of sickle cell anemia we compared patients 11-30 years of age from University of Ibadan, Ibadan, Oyo, Nigeria (n = 214) and University of Illinois at Chicago, Chicago, IL, USA (n = 209). Paralleling findings in the general populations of the two countries, the Chicago patients were more often overweight or obese as defined by the Centers for Disease Control and Prevention (Atlanta, GA, USA) guidelines, and more often had elevated blood pressure (BP) as defined by the National Heart, Lung, and Blood Institute (NHLBI), Bethesda, MD, USA guidelines. The Ibadan patients did not receive the pneumococcal vaccine or hydroxyurea (HU) therapy as frequently as the Chicago patients. Consistent with lower rates of elevated BP and increased body mass index (BMI), stroke history was less frequent in the Ibadan patients ≥18 years old. Furthermore, in combined analyses, systolic and diastolic BP directly correlated with BMI, and elevated weight status independently associated with history of stroke. Our findings are consistent with the possibility that higher values for BMI and BP in Chicago sickle cell anemia patients may contribute to an increased risk of stroke and highlights the need for measures to reduce these risk factors. On the other hand, lower pneumococcal vaccination and HU therapy rates in Ibadan patients highlights the need for more improved vaccination coverage and for studies to define the role of HU therapy in Africa.

Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations

High blood pressure (BP) is more prevalent and contributes to more severe manifestations of cardiovascular disease (CVD) in African Americans than in any other United States ethnic group. Several small African-ancestry (AA) BP genome-wide association studies (GWASs) have been published, but their findings have failed to replicate to date. We report on a large AA BP GWAS meta-analysis that includes 29,378 individuals from 19 discovery cohorts and subsequent replication in additional samples of AA (n = 10,386), European ancestry (EA) (n = 69,395), and East Asian ancestry (n = 19,601). Five loci (EVX1-HOXA, ULK4, RSPO3, PLEKHG1, and SOX6) reached genome-wide significance (p < 1.0 × 10(-8)) for either systolic or diastolic BP in a transethnic meta-analysis after correction for multiple testing. Three of these BP loci (EVX1-HOXA, RSPO3, and PLEKHG1) lack previous associations with BP. We also identified one independent signal in a known BP locus (SOX6) and provide evidence for fine mapping in four additional validated BP loci. We also demonstrate that validated EA BP GWAS loci, considered jointly, show significant effects in AA samples. Consequently, these findings suggest that BP loci might have universal effects across studied populations, demonstrating that multiethnic samples are an essential component in identifying, fine mapping, and understanding their trait variability.

Adrenergic alpha-1 pathway is associated with hypertension among Nigerians in a pathway-focused analysis

Background

The pathway-focused association approach offers a hypothesis driven alternative to the agnostic genome-wide association study. Here we apply the pathway-focused approach to an association study of hypertension, systolic blood pressure (SBP), and diastolic blood pressure (DBP) in 1614 Nigerians with genome-wide data.

Methods and Results

Testing of 28 pathways with biological relevance to hypertension, selected a priori, containing a total of 101 unique genes and 4,349 unique single-nucleotide polymorphisms (SNPs) showed an association for the adrenergic alpha 1 (ADRA1) receptor pathway with hypertension (p<0.0009) and diastolic blood pressure (p<0.0007). Within the ADRA1 pathway, the genes PNMT (hypertension P_gene<0.004, DBP P_gene<0.004, and SBP P_gene<0.009, and ADRA1B (hypertension P_gene<0.005, DBP P_gene<0.02, and SBP P_gene<0.02) displayed the strongest associations. Neither ADRA1B nor PNMT could be the sole mediator of the observed pathway association as the ADRA1 pathway remained significant after removing ADRA1B, and other pathways involving PNMT did not reach pathway significance.

Conclusions

We conclude that multiple variants in several genes in the ADRA1 pathway led to associations with hypertension and DBP. SNPs in ADRA1B and PNMT have not previously been linked to hypertension in a genome-wide association study, but both genes have shown associations with hypertension through linkage or model organism studies. The identification of moderately significant (10⁻²>p>10⁻⁵) SNPs offers a novel method for detecting the “missing heritability” of hypertension. These findings warrant further studies in similar and other populations to assess the generalizability of our results, and illustrate the potential of the pathway-focused approach to investigate genetic variation in hypertension.

Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry

Adult height is a classic polygenic trait of high heritability (h² ∼0.8). More than 180 single nucleotide polymorphisms (SNPs), identified mostly in populations of European descent, are associated with height. These variants convey modest effects and explain ∼10% of the variance in height. Discovery efforts in other populations, while limited, have revealed loci for height not previously implicated in individuals of European ancestry. Here, we performed a meta-analysis of genome-wide association (GWA) results for adult height in 20,427 individuals of African ancestry with replication in up to 16,436 African Americans. We found two novel height loci (Xp22-rs12393627, P = 3.4×10⁻¹² and 2p14-rs4315565, P = 1.2×10⁻⁸). As a group, height associations discovered in European-ancestry samples replicate in individuals of African ancestry (P = 1.7×10⁻⁴ for overall replication). Fine-mapping of the European height loci in African-ancestry individuals showed an enrichment of SNPs that are associated with expression of nearby genes when compared to the index European height SNPs (P<0.01). Our results highlight the utility of genetic studies in non-European populations to understand the etiology of complex human diseases and traits.

Adult height is an ideal phenotype to improve our understanding of the genetic architecture of complex diseases and traits: it is easily measured and usually available in large cohorts, relatively stable, and mostly influenced by genetics (narrow-sense heritability of height h²∼0.8). Genome-wide association (GWA) studies in individuals of European ancestry have identified >180 single nucleotide polymorphisms (SNPs) associated with height. In the current study, we continued to use height as a model polygenic trait and explored the genetic influence in populations of African ancestry through a meta-analysis of GWA height results from 20,809 individuals of African descent. We identified two novel height loci not previously found in Europeans. We also replicated the European height signals, suggesting that many of the genetic variants that are associated with height are shared between individuals of European and African descent. Finally, in fine-mapping the European height loci in African-ancestry individuals, we found SNPs more likely to be associated with the expression of nearby genes than the SNPs originally found in Europeans. Thus, our results support the utility of performing genetic studies in non-European populations to gain insights into complex human diseases and traits.

Significant bacteriuria among asymptomatic antenatal clinic attendees in ibadan, Nigeria

Untreated asymptomatic bacteriuria can lead to urinary tract infection (UTI) in pregnancy with devastating maternal and neonatal effects such as prematurity and low birth weight, higher fetal mortality rates and significant maternal morbidity. We carried out a two year (April 2007 to March 2009) cross-sectional epidemiological study to determine the prevalence of significant bacteriuria among asymptomatic antenatal clinic attendees at two antenatal clinics (ANCs) in University College Hospital and Adeoyo Maternity Hospital, both in Ibadan, Nigeria.

All consenting ANC attendees without UTI were enrolled in the study. Urine specimens of 5 to 10 ml collected from each subject were examined microscopically for white blood cells, red blood cells and bacteria. The specimens were further cultured on MacConkey agar using a sterile bacteriological loop that delivered 0.002 ml of urine. Colony counts yielding bacterial growth of more than 10⁵/ml of pure isolates were considered significant.

Of the 473 subjects studied, 136 had significant bacteriuria, giving a prevalence rate of 28.8%. The highest age specific prevalence (47.8%) was found in the 25–29 year olds while only one (0.7%) was found in the teenage group. A large percentage (64.0%) of subjects with significant bacteriuria had tertiary education, compared with 4.4% who had no formal education but the association was not statistically significant (X² = 0.47, p = 0.79). The majority (75.8%) of subjects with significant bacteriuria had no previous history of abortion, while 20 (14.7%) had one previous abortion and only three (2.1%) admitted to three previous abortions (X² = 5.16, p = 0.16). The majority (69.8%) of those with significant bacteriuria presented at second trimester while 38 (28.0%) presented at third trimester (X² = 6.5, p = 37).

Only 22 (4.6%) of the studied subjects presented at first trimester, and 3 (13.7%) of these had significant bacteriuria.

The prevalence of asymptomatic bacteriuria is high among this study population. Hence we suggest that advocacy programs be initiated to urge pregnant women to access ANC services early in pregnancy.

Urinary pathogens and drug susceptibility patterns of urinary tract infections among antenatal clinic attendees in Ibadan, Nigeria

AIM

To determine the bacterial agents involved in urinary tract infections in pregnant women and their antibiotic susceptibility patterns in Ibadan, Nigeria.

METHODS

All consenting subjects who attended antenatal clinics of the University College Hospital and Adeoyo Maternity Hospital, Ibadan, Nigeria, from 1 April 2007 and 30 March 2009 were interviewed to obtain demographic and pregnancy health data. Mid-stream urine samples obtained were processed by standard methods. Confirmed bacterial isolates were tested against seven antibiotics using the Kirby-Bauer disc diffusion technique.

RESULTS

Of the 473 specimens processed, 136 (28.8%) were positive for microscopy, 118 (25.0%) were culture positive, while 18 (3.8%) were microscopy positive but negative for culture. More than 90% of the bacterial isolates were Gram-negative bacilli, of which approximately 80% were members of the family Enterobacteriaceae. Klebsiella oxytoca accounted for 45 (38.1%) of the causative agents identified, followed by Escherichia coli (31.3%), Pseudomonas aeruginosa (9.3%) and Proteus mirabilis (6.8%). Candida albicans accounted for three (2.6%) of the isolates. Ten isolates (22.2%) of K. oxytoca were resistant to cefuroxime while three (6.7%) were resistant to ofloxacin. The only Gram-positive bacterium isolated, Staphylococcus saprophyticus, accounted for four (4.3%) of all pathogens, of which three (75.0%) were susceptible to nitrofurantoin, ofloxacin, cefuroxime and the amoxicillin-clavulanic acid combination.

CONCLUSIONS

In conclusion, the incidence of culture-positive urinary tract infection in pregnancy is common in Ibadan. More studies are needed to evaluate the susceptibility profile of uropathogens to commonly used antibiotics in our environment.

Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection

The study of recent natural selection in human populations has important applications to human history and medicine. Positive natural selection drives the increase in beneficial alleles and plays a role in explaining diversity across human populations. By discovering traits subject to positive selection, we can better understand the population level response to environmental pressures including infectious disease. Our study examines unusual population differentiation between three large data sets to detect natural selection. The populations examined, African Americans, Nigerians, and Gambians, are genetically close to one another (F(ST) < 0.01 for all pairs), allowing us to detect selection even with moderate changes in allele frequency. We also develop a tree-based method to pinpoint the population in which selection occurred, incorporating information across populations. Our genome-wide significant results corroborate loci previously reported to be under selection in Africans including HBB and CD36. At the HLA locus on chromosome 6, results suggest the existence of multiple, independent targets of population-specific selective pressure. In addition, we report a genome-wide significant (p = 1.36 × 10(-11)) signal of selection in the prostate stem cell antigen (PSCA) gene. The most significantly differentiated marker in our analysis, rs2920283, is highly differentiated in both Africa and East Asia and has prior genome-wide significant associations to bladder and gastric cancers.

Skin changes in patients with chronic renal failure

Management of patients with renal failure remains a major problem in poor-resource nations. Cutaneous manifestations in this group of patients are varied and remain helpful in differentiating acute from chronic renal failure (CRF). We studied the prevalence and pattern of skin disorders in patients with CRF at The University College Hospital, Ibadan, Nigeria, during the period between May 2006 and February 2007. Relevant information was collected with the aid of a questionnaire. The patients were then examined for skin disorders. One hundred and twenty patients who met the inclusion criteria were recruited into the study. The mean age of the CRF patients was 43.12 ± 15.38 years, while that of the control subjects was 43.13 ± 15.38 years. Seventy-six of the 120 patients (63.3%) were on chronic hemodialysis while 44 (36.5%) were on conservative management. A total of 107 patients (89.1%) had at least one skin problem. The skin disorders seen include xerosis in 72 (60%), pruritus in 32 (26.7%), hyperpigmentation, icthyosis and pityriasis versicolor in nine patients each (7.5%), either singly or in combination. Pallor of the skin was seen in three of the patients (2.5%), while uremic frost was seen in one (0.8%). Nail changes were seen in 48 patients (40%). We conclude that xerosis, pruritus, pigmentary and nail changes were the most common skin disorders in patients with CRF in our environment.

Influence of previous abortions and new paternity on the risk of hypertension in nulliparous parturients in Ibadan: a cohort study

AIM

This study aims to determine the influence of previous abortions and new paternity on the risk of hypertension in a cohort of nulliparous women.

METHODS

A prospective cohort study was conducted with development of hypertension in pregnancy as outcome variable. Explanatory variables were previous abortions and paternity. Univariate analysis was by t-test, χ(2) test and Fisher's exact test where applicable. Logistic regression was utilized for multivariate analysis. Stata was utilized for all the analyses. The level of statistical significance was set as P < 0.05.

RESULTS

Same paternity abortions reduced the risk of hypertension (OR 0.48, 95% CI 0.31-0.73). Previous abortions did not reduce the odds of hypertension in pregnancy (OR 1.25, 95% CI 0.83-1.88). Rural dwelling reduced the odds of developing hypertension in pregnancy (OR 0.54, 95% CI 0.42-0.70).

CONCLUSION

The result of this study supports the immunological theory of the etiology of hypertension in pregnancy.

Influence of duration of sexual cohabitation on the risk of hypertension in nulliparous parturients in Ibadan: A cohort study

BACKGROUND

Hypertensive disorders of pregnancy are an important cause of maternal mortality in this environment, it accounts for about 20% of all maternal deaths in pregnancy in Nigeria.

AIM

This study aims to determine the effect of the length of sexual cohabitation on the development of hypertension in pregnancy in a Nigerian population.

MATERIALS AND METHODS

The study was a prospective cohort study; three centres were involved in the study between July 2006 and February 2009. For this study, the main outcome variable was the development of Hypertension in pregnancy. The main explanatory variable was the length of preconception sexual cohabitation. Univariate analysis was by t test, chi-squared test and Fisher's exact test for continuous and categorical variables. Multivariate analysis was by Cox hazard regression.

RESULTS

In the study population, the incidence of gestational hypertension and pre-eclampsia were 28.93% and 4.13% respectively, 29.64% had previous abortions and same paternity abortion rate was 25.92%. Length of sexual cohabitation before index pregnancy was protective against hypertension in pregnancy but not for pre-eclampsia; there was a 4% decrease in the risk of developing hypertension for every month increase in cohabitation (hazard ratio, HR 0.96 (95% CI 0.93-0.99)). Also protective in this model was same paternity abortion with a HR of 0.71 (95% CI 0.55-0.93). A previous abortion was not protective (HR 1.05 (95% CI 0.82-1.35)).

CONCLUSION

It was concluded that increased length of sexual cohabitation prior to conception reduces the risk of gestational hypertension.