Pharmacogenomic implications of the evolutionary history of infectious diseases in Africa.

As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations. Here, we examine Africa's large burden of infectious disease, discuss key examples of known genetic variation modulating disease risk, and provide examples of clinically relevant variants critical for establishing dosing guidelines. We propose that a more systematic characterization of the genetic diversity of African ancestry populations is required if the current benefits of precision medicine are to be extended to these populations.

Pharmacogenomics, ancestry and clinical decision making for global populations.

Pharmacogenomically relevant markers of drug response and adverse drug reactions are known to vary in frequency across populations. We examined minor allele frequencies (MAFs), genetic diversity (FST) and population structure of 1156 genetic variants (including 42 clinically actionable variants) in 212 genes involved in drug absorption, distribution, metabolism and excretion (ADME) in 19 populations (n=1478). There was wide population differentiation in these ADME variants, reflected in the range of mean MAF (ΔMAF) and FST. The largest mean ΔMAF was observed in African ancestry populations (0.10) and the smallest mean ΔMAF in East Asian ancestry populations (0.04). MAFs ranged widely, for example, from 0.93 for single-nucleotide polymorphism (SNP) rs9923231, which influences warfarin dosing to 0.01 for SNP rs3918290 associated with capecitabine metabolism. ADME genetic variants show marked variation between and within continental groupings of populations. Enlarging the scope of pharmacogenomics research to include multiple global populations can improve the evidence base for clinical translation to benefit all peoples.

Conceptualizing human variation.

What is the relationship between the patterns of biological and sociocultural variation in extant humans? Is this relationship accurately described, or best explained, by the term 'race' and the schema of 'racial' classification? What is the relationship between 'race', genetics and the demographic groups of society? Can extant humans be categorized into units that can scientifically be called 'races'? These questions underlie the discussions that address the explanations for the observed differences in many domains between named demographic groups across societies. These domains include disease incidence and prevalence and other variables studied by biologists and social scientists. Here, we offer a perspective on understanding human variation by exploring the meaning and use of the term 'race' and its relationship to a range of data. The quest is for a more useful approach with which to understand human biological variation, one that may provide better research designs and inform public policy.

Transferability and fine-mapping of glucose and insulin quantitative trait loci across populations: CARe, the Candidate Gene Association Resource.

AIMS/HYPOTHESIS: Hyperglycaemia disproportionately affects African-Americans (AfAs). We tested the transferability of 18 single-nucleotide polymorphisms (SNPs) associated with glycaemic traits identified in European ancestry (EuA) populations in 5,984 non-diabetic AfAs. METHODS: We meta-analysed SNP associations with fasting glucose (FG) or insulin (FI) in AfAs from five cohorts in the Candidate Gene Association Resource. We: (1) calculated allele frequency differences, variations in linkage disequilibrium (LD), fixation indices (F(st)s) and integrated haplotype scores (iHSs); (2) tested EuA SNPs in AfAs; and (3) interrogated within ± 250 kb around each EuA SNP in AfAs. RESULTS: Allele frequency differences ranged from 0.6% to 54%. F(st) exceeded 0.15 at 6/16 loci, indicating modest population differentiation. All iHSs were <2, suggesting no recent positive selection. For 18 SNPs, all directions of effect were the same and 95% CIs of association overlapped when comparing EuA with AfA. For 17 of 18 loci, at least one SNP was nominally associated with FG in AfAs. Four loci were significantly associated with FG (GCK, p = 5.8 × 10(-8); MTNR1B, p = 8.5 × 10(-9); and FADS1, p = 2.2 × 10(-4)) or FI (GCKR, p = 5.9 × 10(-4)). At GCK and MTNR1B the EuA and AfA SNPs represented the same signal, while at FADS1, and GCKR, the EuA and best AfA SNPs were weakly correlated (r(2) <0.2), suggesting allelic heterogeneity for association with FG at these loci. CONCLUSIONS/INTERPRETATION: Few glycaemic SNPs showed strict evidence of transferability from EuA to AfAs. Four loci were significantly associated in both AfAs and those with EuA after accounting for varying LD across ancestral groups, with new signals emerging to aid fine-mapping.

Office based muscle biopsy using Vacora vacuum assisted biopsy system.

INTRODUCTION: Muscle biopsy is a minor surgical procedure that has been conducted over several decades in clinical practice. Over the years, the technique to implement this procedure has been modified to make it easier to perform and more tolerable for the patient. This study aimed to assess the feasibility of muscle biopsy as an office based procedure, by using a vacuum Assisted Biopsy System. METHOD: The procedure was successfully carried out on 57 individuals with/without diabetes, currently involved in the African American Diabetes Mellitus Study. One specimen was collected percutaneously from the vastus lateralis, under local anesthesia. A 16-gauge needle was used. RESULTS: Muscle biopsies were successfully carried out on all study participants. The study participants reported no complications after the procedure. CONCLUSION: The findings from our study show that muscle biopsy can be feasibly implemented as an office based procedure, involving minimal muscle invasion, less trauma, hospital stay time, and expenses.

Association of GNB3 C825T polymorphism with peak oxygen consumption.

The C825T single nucleotide polymorphism (SNP) in the guanine nucleotide-binding protein, beta polypeptide 3 ( GNB3) gene gives rise to a splice variant, GNB3s that has enhanced G protein activation and signal transduction activity. This variant has been reported to be associated with cardiovascular disease, diabetes and obesity. We studied this SNP in 95 healthy 18 to 30 year-old African American university students to determine its association with aerobic capacity and cardiorespiratory fitness as measured by peak oxygen consumption (VO (2)peak). We also tested the effect of heart rate variability (HRV) as an independent predictor of VO (2)peak. We tested the association of the SNP and HRV with VO (2)peak in a multivariate regression analysis with appropriate adjustments of covariates, under dominant and recessive models. We found a significant independent association of the 825T allele with VO (2)peak under the dominant model (beta-coef.=-0.101, P=0.0442). We also observed that HRV marginally influenced VO (2)peak. This finding suggests that GNB3 C825T polymorphism is associated with VO (2)peak which is influenced by autonomic modulation of heart rate in African Americans.

Distribution and functional consequences of nucleotide polymorphisms in the 3'-untranslated region of the human Sep15 gene.

Selenium has been shown to prevent cancer in a variety of animal model systems. Both epidemiological studies and supplementation trials have supported its efficacy in humans. However, the mechanism by which selenium suppresses tumor development remains unknown. Selenium is present in known human selenoproteins as the amino acid selenocysteine (Sec). Sec is inserted cotranslationally in response to UGA codons within selenoprotein mRNAs in a process requiring a sequence within the 3'-untranslated region (UTR), referred to as a Sec insertion sequence (SECIS) element. Recently, a human Mr 15,000 selenoprotein (Sep15) was identified that contains an in-frame UGA codon and a SECIS element in the 3'-UTR. Examination of the available cDNA sequences for this protein revealed two polymorphisms located at position 811 (C/T) and at position 1125 (G/A) located within the 3'-UTR. Here, we demonstrate significant differences in Sep15 allele frequencies by ethnicity and that the identity of the nucleotides at the polymorphic sites influences SECIS function in a selenium-dependent manner. This, together with genetic data indicating loss of heterozygosity at the Sep15 locus in certain human tumor types, suggests that Sep15 may be involved in cancer development, risk, or both.

H3Africa multi-centre study of the prevalence and environmental and genetic determinants of type 2 diabetes in sub-Saharan Africa: study protocol.

The burden and aetiology of type 2 diabetes (T2D) and its microvascular complications may be influenced by varying behavioural and lifestyle environments as well as by genetic susceptibility. These aspects of the epidemiology of T2D have not been reliably clarified in sub-Saharan Africa (SSA), highlighting the need for context-specific epidemiological studies with the statistical resolution to inform potential preventative and therapeutic strategies. Therefore, as part of the Human Heredity and Health in Africa (H3Africa) initiative, we designed a multi-site study comprising case collections and population-based surveys at 11 sites in eight countries across SSA. The goal is to recruit up to 6000 T2D participants and 6000 control participants. We will collect questionnaire data, biophysical measurements and biological samples for chronic disease traits, risk factors and genetic data on all study participants. Through integrating epidemiological and genomic techniques, the study provides a framework for assessing the burden, spectrum and environmental and genetic risk factors for T2D and its complications across SSA. With established mechanisms for fieldwork, data and sample collection and management, data-sharing and consent for re-approaching participants, the study will be a resource for future research studies, including longitudinal studies, prospective case ascertainment of incident disease and interventional studies.

The need for an integrated approach for chronic disease research and care in Africa.

With the changing distribution of infectious diseases, and an increase in the burden of non-communicable diseases, low- and middle-income countries, including those in Africa, will need to expand their health care capacities to effectively respond to these epidemiological transitions. The interrelated risk factors for chronic infectious and non-communicable diseases and the need for long-term disease management, argue for combined strategies to understand their underlying causes and to design strategies for effective prevention and long-term care. Through multidisciplinary research and implementation partnerships, we advocate an integrated approach for research and healthcare for chronic diseases in Africa.

Beta cell function and response to treatment in Nigerians with Type 2 diabetes mellitus.

There are scant data from African populations on the association between beta-cell function and response to treatment with oral hypoglycaemic agents in Type 2 diabetes mellitus (T2DM). Fasting plasma C-peptide (FCP) and glucagon-stimulated C-peptide (GSCP) levels were measured in 116 Nigerians with T2DM at a university teaching hospital. After 9 months of follow-up and treatment, they were categorized into three groups based on response to treatment: (A) good control but not on maximum sulphonylurea (SU) therapy, (B) inadequate control but not on maximum SU therapy and (C) on maximum SU therapy+/-insulin or biguanide. Logistic regression models were used to investigate how well C-peptide levels predicted the subjects belonging to Group C who are likely to require insulin. The mean FCP and mean GSCP levels of Group C were significantly lower than in the other groups (p=0.024; p= <0.001 respectively). A GSCP cut-off value of < or =1.3 ng/mL predicted membership of Group C with 85% sensitivity and 89% specificity while a cut-off of < or =1.8 ng/mL was associated with 91% sensitivity and 66% specificity. In resource-poor settings where inadequate treatment are common, estimation of GSCP may be useful in predicting treatment response and should be weighed against the cost of inadequate therapy with higher morbidity and mortality.

Association of waist circumference with risk of hypertension and type 2 diabetes in Nigerians, Jamaicans, and African-Americans.

OBJECTIVE: Prior studies have supported that waist circumference correlates better with visceral adipose tissue and is a better predictor of cardiovascular disease than are BMI and waist-to-hip ratio. In this study, we reexamine the role of waist size on the risk of hypertension and type 2 diabetes in African-origin populations from three contrasting environments. RESEARCH DESIGN AND METHODS: A cross-sectional survey was conducted of 5,042 men and women 25-74 years of age from Nigeria, Jamaica, and the U.S. The relationship between waist, blood pressure, and fasting blood glucose was assessed using multiple linear regression analyses. Logistic regression analyses using sex-specific empirical waist cut-points were used to determine the risks of hypertension and type 2 diabetes. RESULTS: Waist circumference was positively correlated with blood pressure and fasting blood glucose (P < 0.05). Increasing waist quartiles were significantly associated with higher risks of hypertension in the three populations, as estimated from age-adjusted odds ratios obtained from sex-specific logistic regression models. A highly elevated risk of type 2 diabetes-10-fold for Jamaican men and 23-fold for African-American women-was observed in the comparison of lowest to highest quartiles of waist circumference. CONCLUSIONS: Substantial reduction in hypertension and diabetes in men and women is achievable if the waist size is decreased in these populations. Intervention programs designed to reduce waist circumference through lifestyle modification, including exercise and diet, may have significant public health significance in reducing the incidence of hypertension and adult-onset diabetes in these populations.

Prevalence of NIDDM among populations of the African diaspora.

OBJECTIVE: Rates of non-insulin-dependent diabetes mellitus have risen sharply in recent years among blacks in the U.S. and the U.K. Increases in risk have likewise been observed in the island nations of the Caribbean and in urban West Africa. To date, however, no systematic comparison of the geographic variation of NIDDM among black populations has been undertaken. RESEARCH DESIGN AND METHODS: In the course of an international collaborative study on cardiovascular disease, we used a standardized protocol to determine the rates of NIDDM and associated risk factors in populations of the African diaspora. Representative samples were drawn from sites in Nigeria, St. Lucia, Barbados, Jamaica, the United States, and the United Kingdom. A total of 4,823 individuals aged 25-74 years were recruited, all sites combined. RESULTS: In sharp contrast to a prevalence of 2% in Nigeria, age-adjusted prevalences of self-reported NIDDM were 9% in the Caribbean and 11% in the U.S. and the U.K. Mean BMI ranged from 22 kg/m2 among men in West Africa to 31 kg/m2 in women in the U.S. Disease prevalence across sites was essentially collinear with obesity, pointing to site differences in the balance between energy intake and expenditure as the primary determinant of differential NIDDM risk among these populations. CONCLUSIONS: In ethnic groups sharing a common genetic ancestry, these comparative data demonstrate the determining influence of changes in living conditions on the population risk of NIDDM.

Maximum-likelihood generalized heritability estimate for blood pressure in Nigerian families.

Elevated blood pressure (BP) is more common in relatives of hypertensives than in relatives of normotensives, indicating familial resemblance of the BP phenotypes. Most published studies have been conducted in westernized societies. To assess the ability to generalize these estimates, we examined familial patterns of BP in a population-based sample of 510 nuclear families, including 1552 individuals (320 fathers, 370 mothers, 475 sons, and 387 daughters) from Ibadan, Nigeria. The prevalence of obesity in this community is low (body mass index: fathers, 21.6; mothers, 23.6; sons, 19.2; and daughters=21.0 kg/m2). The BP phenotype used in all analyses was created from the best regression model by standardizing the age-adjusted systolic blood pressure (SBP) and diastolic blood pressure (DBP) to 0 mean and unit variance. Heritability was estimated by use of the computer program SEGPATH from the most parsimonious model of "no spouse and neither gender nor generation difference" as 45% for SBP and 43% for DBP. The lack of a significant spouse correlation is consistent with little or no influence of the common familial environment. However, the heritability estimate of <50% for both SBP and DBPs reinforces the importance of the nonshared environmental effect.

Leptin and body composition of Nigerians, Jamaicans, and US blacks.

The role of leptin in humans remains controversial. Leptin concentrations are highly correlated with body fat stores. We tested whether or not this relation was consistent across the range of body composition encompassing the lean as well as the obese. Individuals participating in community-based comparative research in Nigeria (n = 363), Jamaica (n = 372), and the United States (Maywood, IL; n = 699) had their plasma leptin concentrations and body compositions (with bioelectrical impedance analysis) measured. All participants identified themselves as being black. Body mass index (in kg/m2) ranged from 14 to 62. Large differences in mean plasma leptin were noted across populations for both men and women in Nigeria, Jamaica, and the United States, respectively (men: 2.8, 3.9, and 6.8 microg/L; women: 10.3, 18.6, and 27.7 microg/L). An exponential function fit the relation between percentage body fat or total fat mass and leptin for men and women at each site. For women and men the exponential function with either percentage body fat or total fat mass was of the same shape, but increased by a constant in women, yielding higher leptin concentrations than in men at every level of body fat. On the basis of this broad distribution of body composition, the data suggest an exponential response of leptin to increases in body fat stores, consistent with the development of leptin resistance in individuals developing obesity. These findings likewise confirm that men and women exhibit different set points in terms of leptin production.

Abdominal adiposity and clustering of multiple metabolic syndrome in White, Black and Hispanic americans.

PURPOSE: The aim of this study was to evaluate the association of abdominal adiposity assessed by waist circumference (WC) with clustering of multiple metabolic syndromes (MMS) in White, Black and Hispanic Americans. MMS was defined as the occurrence of two or more of either hypertension, type 2 diabetes mellitus, dyslipidemia, hypertriglyceridemia or hyperinsulinemia. METHODS: The number of MMS and fasting insulin (a surrogate measure of MMS) were each used as dependent variables in gender-specific multiple linear regression models, adjusting for age, smoking and alcohol intake. The contribution of WC to interethnic differences in clustering of MMS and fasting insulin concentration was assessed in gender-specific linear regression models. The risk of MMS due to large waist was estimated by comparing odds ratio for men with WC >/= 102 cm with those with WC < 102, and women with WC >/= 88 cm with women with WC < 88 cm in the logistic regression model adjusting for age, smoking and alcohol intake. RESULTS: WC was positively and independently associated with clustering of MMS and increased fasting insulin concentration adjusting for age, smoking and alcohol intake in the three ethnic groups (p < 0.01). Black ethnicity was associated with clustering of MMS and fasting insulin concentration (p < 0.01). Hispanic ethnicity was also associated with clustering of MMS in men and associated with fasting insulin concentration in both men and women (p < 0.01). In both men and women, the risk of MMS clustering was strongly associated with increased WC in all ethnic groups independent of BMI. CONCLUSION: WC appears to be a marker for multiple metabolic syndromes in these ethnic groups. The results of this investigation lend support to the view that waist measurement should be considered as a clinical variable for assessing the risk of cardiovascular diseases.

In search of susceptibility genes for type 2 diabetes in West Africa: the design and results of the first phase of the AADM study.

PURPOSE: The purpose of this study is to map type 2 diabetes susceptibility genes in West African ancestral populations of African-Americans, through an international collaboration between West African and US investigators. DESIGN AND METHODS: Affected sib-pairs (ASP) along with unaffected spouse controls are being enrolled and examined in West Africa, with two sites established in Ghana (Accra and Kumasi) and three in Nigeria (Enugu, Ibadan, and Lagos). Eligible participants are invited to study clinics to obtain detailed epidemiologic, family, and medical history information. Blood samples are drawn from each participant to measure glucose, insulin, C-peptide, total cholesterol, LDL, HDL, triglycerides, albumin, creatinine, urea, uric acid, total calcium and to detect autoantibodies to glutamic acid decarboxylase (GAD). DNA is isolated from frozen white blood cells obtained from 20 ml of EDTA whole blood samples. RESULTS: With full informed consent, 162 individuals from 78 families have been enrolled and examined since the Africa America Diabetes Mellitus (AADM) study began in June of 1997. Logistics of field examinations and specimen shipping have been successfully established. At the end of the third year of field activity (September 2000) the AADM study will have enrolled and performed comprehensive examination on 400 ASP with type 2 diabetes, for a minimum of 800 cases and 200 controls from Ghana and Nigeria. At the current participation rate, the goal of 400 sib-pairs and 200 controls will be met before the scheduled closing date. CONCLUSIONS: The AADM study will create a comprehensive epidemiologic and genetic resource that will facilitate a powerful genome-wide search for West African susceptibility genes to type 2 diabetes.

Predictive values of waist circumference for dyslipidemia, type 2 diabetes and hypertension in overweight White, Black, and Hispanic American adults.

Waist circumferences (WC) >/=102 cm for men and >/=88 cm for women have been proposed by an expert panel as cut-points for identifying increased risk for the development of obesity comorbidities for most adults. The aim of this investigation was to examine the predictive values of these WC cut-points for hypercholesterolemia, low concentration of high (HDL-C), and high concentration of low (LDL-C) density lipoprotein cholesterol, hypertriglyceridemia, type 2 diabetes, and hypertension in overweight American adults. Data from NHANES III were utilized for the analysis. Predictive abilities were determined by calculating sensitivity, specificity, positive (PV+) and negative (PV-) predictive values in overweight subjects with BMI 25-29.9 kg/m(2). Sensitivity of WC cut-point was stronger for high LDL-C compared to other risk factors with the highest values recorded in the 40-59 and 60-69 year age groups in men and women, respectively. PV+ of WC cut-points for dyslipidemia, type 2 diabetes, and hypertension were low in men compared to women. PV+ tended to increase with age, from 19-39, 40-59 to 60-90 year age groups in Whites, Blacks, and Hispanic men. In men, the highest PV+ were recorded for hypertriglyceridemia in the 60-90 years old groups, with values of 71.6%, 52.5%, and 43.3% in Whites, Blacks, and Hispanics, respectively. The CVD risk factor associated with the highest PV+ in women was diabetes with values of 97.2% in Whites and 88.9% in Blacks, and hypertriglyceridemia with a value of 93.8% in the 17-39 year age group in Hispanics. Among Black men 40-59 years of age, only 32% of a population of overweight hypertensives were detected by the WC cut-points, and among Black women, 40-59 years of age, only 54% were detected. Given the low sensitivity of these cut-points for detecting hypertension, one of the major co-morbidities of obesity, these cut-points failed to provide adequate evidence for the use of WC in determining or evaluating patients as to co-morbid states. We recommend further studies to determine a set of specific cut-points associated with increased risk of CVD in different population groups.

Absence of black-white differences in sodium and calcium in platelets.

Consistent differences in sodium transport in red blood cells are observed in blacks compared to whites and have been the basis for speculation regarding physiologic differences in the vascular bed as well. The theoretical link between these metabolic markers and the risk of hypertension generally assumes a secondary effect on calcium. Calcium metabolism in red cells is difficult to study, however, so this proposition has never been tested directly. Given the growing importance of platelets in this area of research, and the availability of sensitive laboratory methods, we carried out a systematic examination of calcium and sodium homeostasis in this cell line among black and white normotensive subjects. No differences were noted in resting cytosolic calcium, mobilizable stores, agonist-induced response, or sodium-calcium exchange. In addition, resting sodium was not different between groups, nor was the increase in sodium induced by ouabain. A correlation of 0.3 was observed between blood pressure and both resting and stimulated cytosolic calcium (P < .05). Red cells may be atypical for studies of calcium and sodium homeostasis, and their relevance for interethnic studies of causal pathways in hypertension should be reconsidered.

Lack of association between a biallelic polymorphism in the adducin gene and blood pressure in whites and African Americans.

Population-based candidate gene association analyses are becoming increasingly popular as a result of a greater number of genes and gene polymorphisms having been identified for which some functional information is available. Because many biochemical and physiologic systems impact blood pressure regulation and hypertension susceptibility, many of these identified genes and polymorphisms are candidates for population-level association studies involving blood pressure levels or hypertension status. Recent studies have suggested that the alpha-adducin gene may harbor polymorphisms that influence blood pressure level. Therefore, we embarked on a study to test one such polymorphism in two large US samples: one from an urban African American population (Maywood, IL) and another from a rural white population (Tecumseh, MI). We used both family-based association tests and tests that consider the impact of additional measured factors beyond adducin gene variation on blood pressure levels. We found no evidence for a significant effect of the chosen adducin polymorphism on blood pressure variation in either sample. We also found no association between Adducin genotypes and antihypertensive use. These facts, together with similar findings in companion studies, suggest that the alpha-adducin gene polymorphism does not have a pronounced effect on blood pressure variation in the populations studied. This does not suggest, however, that the alpha-adducin gene does not have a role in blood pressure regulation and hypertension susceptibility.

The mortality risk associated with hypertension: preliminary results of a prospective study in rural Nigeria.

The contribution of hypertension to adult mortality in Africa has not been well studied. Although cross-sectional surveys have provided data on the prevalence of this condition, the relative risk of death associated with hypertension has not been defined. In the face of high levels of competing mortality from infectious disease among the general population, and the virtual absence of atherosclerotic precursors, estimates of risk derived from industrialised countries may not be generalisable to this setting. We conducted a 2-year prospective study among 1344 mean and women in a rural community in south-western Nigeria. The prevalence of hypertension (140/90 mm Hg) at baseline was 9.3%. In the observational phase, 3.0% of the survey participants died each year. Among the 74 decedents, hypertension was nearly twice as common as among those who survived (14.9% vs 8.4%). In multivariate analysis the risk of death increased over 60% for a 20 mm Hg increase in diastolic blood pressure. The population attributable risk, or the reduction in mortality that would have been observed if hypertension were not present in this community, was estimated as 7%. These findings document an identifiable impact of hypertension on all-cause mortality in rural Africa and demonstrate that programs to evaluate potential treatment options are needed.