Background

It has been suggested that adiponectin may offer protection against the adverse health effects of obesity. In this study, we determined the prevalence of paradoxically high adiponectin or paradoxical hyperadiponectinemia (PHA) among obese African Americans and investigated its relationship with the metabolically healthy obese (MHO) phenotype.

Methods

Total adiponectin and metabolic markers including fasting glucose, insulin, serum lipids and obesity measures were determined in 822 unrelated participants from the Howard University Family Study (HUFS). Logistic regression models were used to evaluate the association between MHO phenotype and PHA while adjusting for relevant covariates.

Results

Overall, men had significantly lower adiponectin levels than women. However, adiponectin level was associated with obesity measures, glucose, insulin and insulin resistance index in both men and women. Equal proportion of the obese male and female subjects (19.2%; 66/343) had PHA; these obese individuals with PHA had a healthier metabolic profile including higher HDL-cholesterol, lower insulin levels and smaller waist circumference and insulin levels compared to those without PHA. Also, 28% (96/343) of the study participants met the criteria of MHO phenotype. Interestingly, 42% (28/66) of the obese individuals with PHA also had the MHO phenotype. Finally, the MHO phenotype was associated with PHA in both men and women.

Conclusions

These findings confirm the presence of MHO in African Americans and demonstrate the association of PHA with the MHO phenotype. In all, our findings along with other published results provide evidence for a more systematic investigation of the mechanisms underlying the protective function of adiponectin and its potential therapeutic applications in human metabolic disorders.

Although waist circumference (WC) is a marker of visceral adipose tissue (VAT), WC cut-points are based on BMI category. We compared WC–BMI and WC–VAT relationships in blacks and whites. Combining data from five studies, BMI and WC were measured in 1,409 premenopausal women (148 white South Africans, 607 African–Americans, 186 black South Africans, 445 West Africans, 23 black Africans living in United States). In three of five studies, participants had VAT measured by computerized tomography (n = 456). Compared to whites, blacks had higher BMI (29.6 ± 7.6 (mean ± s.d.) vs. 27.6 ± 6.6 kg/m2, P = 0.001), similar WC (92 ± 16 vs. 90 ± 15 cm, P = 0.27) and lower VAT (64 ± 42 vs. 101 ± 59 cm2, P < 0.001). The WC–BMI relationship did not differ by race (blacks: β (s.e.) WC = 0.42 (.01), whites: β (s.e.) WC = 0.40 (0.01), P = 0.73). The WC–VAT relationship was different in blacks and whites (blacks: β (s.e.) WC = 1.38 (0.11), whites: β (s.e.) WC = 3.18 (0.21), P < 0.001). Whites had a greater increase in VAT per unit increase in WC. WC–BMI and WC–VAT relationships did not differ among black populations. As WC–BMI relationship did not differ by race, the same BMI-based WC guidelines may be appropriate for black and white women. However, if WC is defined by VAT, race-specific WC thresholds are required.

BACKGROUND

Podoconiosis is a tropical lymphedema resulting from long-term barefoot exposure to red-clay soil derived from volcanic rock. The World Health Organization recently designated it as a neglected tropical disease. Podoconiosis develops in only a subgroup of exposed people, and studies have shown familial clustering with high heritability (63%).

METHODS

We conducted a genomewide association study of 194 case patients and 203 controls from southern Ethiopia. Findings were validated by means of family-based association testing in 202 family trios and HLA typing in 94 case patients and 94 controls.

RESULTS

We found a genomewide significant association of podoconiosis with the single-nucleotide polymorphism (SNP) rs17612858, located 5.8 kb from the HLA-DQA1 locus (in the allelic model: odds ratio, 2.44; 95% confidence interval [CI], 1.82 to 3.26; P = 1.42×10−9; and in the additive model: odds ratio, 2.19; 95% CI, 1.66 to 2.90; P = 3.44×10−8), and suggestive associations (P<1.0×10−5) with seven other SNPs in or near HLA-DQB1, HLA-DQA1, and HLA-DRB1. We confirmed these associations using family-based association testing. HLA typing showed the alleles HLA-DRB1*0701 (odds ratio, 2.00), DQA1*0201 (odds ratio, 1.91), and DQB1*0202 (odds ratio, 1.79) and the HLA-DRB1*0701–DQB1*0202 haplotype (odds ratio, 1.92) were risk variants for podoconiosis.

CONCLUSIONS

Association between variants in HLA class II loci with podoconiosis (a noncommuni-cable disease) suggests that the condition may be a T-cell–mediated inflammatory disease and is a model for gene–environment interactions that may be relevant to other complex genetic disorders. (Funded by the Wellcome Trust and others.)

Advances in technology and reduced costs are facilitating large-scale sequencing of genes and exomes as well as entire genomes. Recently, we described an approach based on haplotypes called SCARVA1 that enables the simultaneous analysis of the association between rare and common variants in disease etiology. Here, we describe an extension of SCARVA that evaluates individual markers instead of haplotypes. This modified method (SCARVAsnp) is implemented in four stages. First, all common variants in a pre-specified region (eg, gene) are evaluated individually. Second, a union procedure is used to combined all rare variants (RVs) in the index region, and the ratio of the log likelihood with one RV excluded to the log likelihood of a model with all the collapsed RVs is calculated. On the basis of previously-reported simulation studies,1 a likelihood ratio ≥1.3 is considered statistically significant. Third, the direction of the association of the removed RV is determined by evaluating the change in λ values with the inclusion and exclusion of that RV. Lastly, significant common and rare variants, along with covariates, are included in a final regression model to evaluate the association between the trait and variants in that region. We apply simulated and real data sets to show that the method is simple to use, computationally effcient, and that it can accurately identify both common and rare risk variants. This method overcomes several limitations of existing methods. For example, SCARVAsnp limits loss of statistical power by not including variants that are not associated with the trait of interest in the final model. Also, SCARVAsnp takes into consideration the direction of association by effectively modelling positively and negatively associated variants.

Purpose

Deficiency of prolyl 3-hydroxylase 1, encoded by LEPRE1, causes recessive osteogenesis imperfecta. We previously identified a LEPRE1 mutation, exclusively in African Americans and contemporary West Africans. We hypothesized that this allele originated in West Africa and was introduced to the Americas with the Atlantic slave trade. We aimed to determine the frequency of carriers for this mutation among African Americans and West Africans, and the mutation origin and age.

Methods

Genomic DNA was screened for the mutation using PCR and restriction digestion, and a custom TaqMan genomic SNP assay. The mutation age was estimated using microsatellites and short tandem repeats spanning 4.2 Mb surrounding LEPRE1 in probands and carriers.

Results

Approximately 0.4% of Mid-Atlantic African Americans carry this mutation, estimating recessive OI in 1/260,000 births in this population. In Nigeria and Ghana, 1.48% of unrelated individuals are heterozygous carriers, predicting 1/18,260 births will be affected with recessive OI, equal to the incidence of de novo dominant OI. The mutation was not detected in Africans from surrounding countries. All carriers shared a haplotype of 63-770 Kb, consistent with a single founder for this mutation. Using linkage disequilibrium analysis, the mutation was estimated to have originated between 650 and 900 years before present (1100-1350 C.E.).

Conclusions

We identified a West African founder mutation for recessive OI in LEPRE1. Nearly 1.5% of Ghanians and Nigerians are carriers. The age of this allele is consistent with introduction to North America via the Atlantic slave trade (1501 – 1867 C.E).

Recent developments in high-throughput genotyping and whole-genome sequencing will enhance the identification of disease loci in admixed populations. We discuss how a more refined estimation of ancestry benefits both admixture mapping and association mapping, making disease loci identification in admixed populations more powerful.

High-throughput genotyping and sequencing will enable refined estimation of ancestry, thus enhancing disease loci identification in admixed populations

Total serum bilirubin is associated with several clinical outcomes, including cardiovascular disease, diabetes and drug metabolism. We conducted a genome-wide association study in 619 healthy unrelated African Americans in an attempt to replicate reported findings in Europeans and Asians and to identify novel loci influencing total serum bilirubin levels. We analyzed a dense panel of over two million genotyped and imputed SNPs in additive genetic models adjusting for age, sex, and the first two significant principal components from the sample covariance matrix of genotypes. Thirty-nine SNPs spanning a 78 kb region within the UGT1A1 displayed P-values <5 × 10−8. The lowest P-value was 1.7 × 10−22 for SNP rs887829. None of SNPs in the UGT1A1 remained statistically significant in conditional association analyses that adjusted for rs887829. In addition, SNP rs10929302 located in phenobarbital response enhancer module was significantly associated with bilirubin level with a P-value of 1.37 × 10−11; this enhancer module is believed to have a critical role in phenobarbital treatment of hyperbilirubinemia. Interestingly, the lead SNP, rs887829, is in strong linkage disequilibrium (LD) (r2≥0.74) with rs10929302. Taking advantage of the lower LD and shorter haplotypes in African-ancestry populations, we identified rs887829 as a more refined proxy for the causative variant influencing bilirubin levels. Also, we replicated the reported association between variants in SEMA3C and bilirubin levels. In summary, UGT1A1 is a major locus influencing bilirubin levels and the results of this study promise to contribute to understanding of the etiology and treatment of hyperbilirubinaemia in African-ancestry populations.

For samples of admixed individuals, it is possible to test for both ancestry effects via admixture mapping and genotype effects via association mapping. Here, we describe a joint test called BMIX that combines admixture and association statistics at single markers. We first perform high-density admixture mapping using local ancestry. We then perform association mapping using stratified regression, wherein for each marker genotypes are stratified by local ancestry. In both stages, we use generalized linear models, providing the advantage that the joint test can be used with any phenotype distribution with an appropriate link function. To define the alternative densities for admixture mapping and association mapping, we describe a method based on autocorrelation to empirically estimate the testing burdens of admixture mapping and association mapping. We then describe a joint test that uses the posterior probabilities from admixture mapping as prior probabilities for association mapping, capitalizing on the reduced testing burden of admixture mapping relative to association mapping. By simulation, we show that BMIX is potentially orders-of-magnitude more powerful than the MIX score, which is currently the most powerful frequentist joint test. We illustrate the gain in power through analysis of fasting plasma glucose among 922 unrelated, non-diabetic, admixed African Americans from the Howard University Family Study. We detected loci at 1q24 and 6q26 as genome-wide significant via admixture mapping; both loci have been independently reported from linkage analysis. Using the association data, we resolved the 1q24 signal into two regions. One region, upstream of the gene FAM78B, contains three binding sites for the transcription factor PPARG and two binding sites for HNF1A, both previously implicated in the pathology of type 2 diabetes. The fact that both loci showed ancestry effects may provide novel insight into the genetic architecture of fasting plasma glucose in individuals of African ancestry.

Author Summary

Most genome-wide association studies performed to date have focused on individuals with European ancestry. Admixed African Americans tend to have disproportionately higher risk for many common, complex diseases. Disease or trait mapping in admixed individuals can benefit from joint analysis of ancestry and genotype effects. We developed a joint test that is more powerful than either admixture mapping of ancestry effects or association mapping of genotype effects performed separately. Our joint test fully capitalizes on the reduced testing burden of admixture mapping relative to association mapping. The test is based on generalized linear models and can be performed using standard statistical software. We illustrate the increased power of the joint test by detecting two loci for fasting plasma glucose in a sample of unrelated African American individuals, neither of which loci was detected as significant by traditional association analysis.

Two single nucleotide polymorphisms (SNPs), rs4415084, and rs10941679 on chromosome 5p12 were associated with risk of breast cancer in a recent genome-wide association study (GWAS) of women of European ancestry. Both SNPs are located in a large high-LD region and the causal variant(s) are still unknown. We conducted a nested case–control study in a cohort of African American women to replicate and narrow the region carrying the causal variant(s). We evaluated 14 tagging SNPs in a 98 kb LD block surrounding the index SNPs in 886 breast cancer cases and 1,089 controls from the Black Women's Health Study. We used the Cochran–Armitage trend test to assess association with breast cancer risk. Odds ratios were derived from logistic regression analyses adjusted for potential confounders including percent European admixture. We confirmed the reported association of rs4415084 SNP with overall risk of breast cancer (P = 0.06), and, as in the original study, observed a stronger association with estrogen receptor positive tumors (P = 0.03). We identified four other SNPs (rs6451770, rs12515012, rs13156930, and rs16901937) associated with risk of breast cancer at the nominal alpha value of 0.05; all of them were located in a 59 kb HapMap YRI LD block. After correction for multiple testing, the association with SNP rs16901937 remained significant (P permutated = 0.038). The G allele was associated with a 21% increased risk of breast cancer overall and with a 32% increase in tumors positive for both estrogen and progesterone receptors. The present results from an African ancestry (AA) population confirm the presence of breast cancer susceptibility genetic variants in the chromosome 5p12 region. We successfully used the shorter range of LD in our AA sample to refine the localization of the putative causal variant.

Background

Although designed to predict cardiovascular disease and type 2 diabetes mellitus, the Metabolic Syndrome (MetSyn) under-predicts these conditions in African-Americans (AA). Failure of MetSyn in AA is often attributed to their relative absence of hypertriglyceridemia. It is unknown if the African experience with MetSyn will be similar or different to that in AA. Focusing on the lipid profile, our goal was to determine in West Africans (WA) and AA the pattern of variables that leads to the diagnosis of the MetSyn.

Methods

Cross-sectional analysis of 1296 subjects (364 WA, 44% male, 932 AA, 46% male). WA were from urban centers in Nigeria and Ghana and enrolled in the Africa America Diabetes Mellitus Study. AA lived in Washington, DC and participated in the Howard University Family Study.

Results

The prevalence of MetSyn was different in WA women and men: 42% vs.19%, P<0.001, and in AA women and men: 25% vs.17%, P<0.01. The three variables that most often led to the diagnosis of MetSyn in WA and AA were: low HDL-C, central obesity and hypertension. Less than 40% of AA and less than 25% of WA with the MetSyn had hypertriglyceridemia.

Conclusions

Elevated triglyceride levels were uncommon in both WA and AA with MetSyn. As the relative absence of hypertriglyceridemia is associated with a lack of efficacy of MetSyn in AA, caution is warranted in diagnosing MetSyn in WA, the ancestral population of AA. Prospective studies are necessary to determine if an ethnic-specific reformulation of the MetSyn scoring system for lipids might optimize risk identification in black populations.

SUMMARY

Osteogenesis imperfecta is a heritable disorder that causes bone fragility. Mutations in type I collagen result in autosomal dominant osteogenesis imperfecta, whereas mutations in either of two components of the collagen prolyl 3-hydroxylation complex (cartilage-associated protein [CRTAP] and prolyl 3-hydroxylase 1 [P3H1]) cause autosomal recessive osteogenesis imperfecta with rhizomelia (shortening of proximal segments of upper and lower limbs) and delayed collagen folding. We identified two siblings who had recessive osteogenesis imperfecta without rhizomelia. They had a homozygous start-codon mutation in the peptidyl-prolyl isomerase B gene (PPIB), which results in a lack of cyclophilin B (CyPB), the third component of the complex. The proband’s collagen had normal collagen folding and normal prolyl 3-hydroxylation, suggesting that CyPB is not the exclusive peptidyl-prolyl cis–trans isomerase that catalyzes the rate-limiting step in collagen folding, as is currently thought.

The African Society of Human Genetics (AfSHG), founded in 2003 with its inaugural meeting in Accra, Ghana,1 has the stated missions of (1) disseminating information about human genetics research in Africa, (2) establishing a mentorship network providing educational resources, including the development of appropriate technology transfer, (3) providing advocacy for human genetic research in Africa, and (4) encouraging collaborative research. Despite its young age, the AfSHG has developed a strong cadre of active researchers, both within and outside of Africa, with more than 400 members (from 16 countries across Africa as well as 8 other countries), and has held six successful meetings, five in Africa and one in the United States.

Imputation of genotypes for markers untyped in a study sample has become a standard approach to increase genome coverage in genome-wide association studies at practically zero cost. Most methods for imputing missing genotypes extend previously described algorithms for inferring haplotype phase. These algorithms generally fall into three classes based on the underlying model for estimating the conditional distribution of haplotype frequencies: a cluster-based model, a multinomial model, or a population genetics-based model. We compared BEAGLE, PLINK, and MACH, representing the three classes of models, respectively, with specific attention to measures of imputation success and selection of the reference panel for an admixed study sample of African Americans. Based on analysis of chromosome 22 and after calibration to a fixed level of 90% concordance between experimentally determined and imputed genotypes, MACH yielded the largest absolute number of successfully imputed markers and the largest gain in coverage of the variation captured by HapMap reference panels. Following the common practice of performing imputation once, the Yoruba in Ibadan, Nigeria (YRI) reference panel outperformed other HapMap reference panels, including 1) African ancestry from Southwest USA (ASW) data, 2) an unweighted combination of the Northern and Western Europe (CEU) and YRI data into a single reference panel, and 3) a combination of the CEU and YRI data into a single reference panel with weights matching estimates of admixture proportions. For our admixed study sample, the optimal strategy involved imputing twice with the HapMap CEU and YRI reference panels separately and then merging the data sets.

Genomic science and associated technologies are facilitating an unprecedented rate of discovery of novel insights into the relationship between human genetic variation and health. The willingness of large numbers of individuals from different ethnic and cultural backgrounds to donate biological samples is one of the major factors behind the success of the ongoing genomic revolution. Although current informed consent documents and processes demonstrate a commitment to ensuring that study participants are well informed of the risks and benefits of participating in genomic studies, there continues to be a need to develop effective new approaches for adequately informing participants of the changing complexities of the scientific and ethical issues that arise in the conduct of genomics research. Examples of these complexities in genomic research include more widespread use of whole-genome sequencing technologies, broad sharing of individual-level data, evolving information technology, the growing demand for the return of genetic results to participants, and changing attitudes about privacy and the expansion of genomics studies to global populations representing diverse cultural, linguistic and socio-economic backgrounds. We highlight and briefly discuss the importance of ten core scientific, cultural and social factors that are particularly relevant to tailoring informed consent in genomic research, and we draw attention to the need for the informed consent document and process to be responsive to the evolving nature of genomic research.

Genome-wide association studies have identified hundreds of genetic variants associated with complex human diseases and traits, and have provided valuable insights into their genetic architecture. Most variants identified so far confer relatively small increments in risk, and explain only a small proportion of familial clustering, leading many to question how the remaining, ‘missing’ heritability can be explained. Here we examine potential sources of missing heritability and propose research strategies, including and extending beyond current genome-wide association approaches, to illuminate the genetics of complex diseases and enhance its potential to enable effective disease prevention or treatment.

Human height is the prototypical polygenic quantitative trait. Recently, several genetic variants influencing adult height were identified, primarily in individuals of East Asian (Chinese Han or Korean) or European ancestry. Here, we examined 152 genetic variants representing 107 independent loci previously associated with adult height for transferability in a well-powered sample of 1,016 unrelated African Americans. When we tested just the reported variants originally identified as associated with adult height in individuals of East Asian or European ancestry, only 8.3% of these loci transferred (p-values≤0.05 under an additive genetic model with directionally consistent effects) to our African American sample. However, when we comprehensively evaluated all HapMap variants in linkage disequilibrium (r2≥0.3) with the reported variants, the transferability rate increased to 54.1%. The transferability rate was 70.8% for associations originally reported as genome-wide significant and 38.0% for associations originally reported as suggestive. An additional 23 loci were significantly associated but failed to transfer because of directionally inconsistent effects. Six loci were associated with adult height in all three groups. Using differences in linkage disequilibrium patterns between HapMap CEU or CHB reference data and our African American sample, we fine-mapped these six loci, improving both the localization and the annotation of these transferable associations.

Background

The consent process for a genetic study is challenging when the research is conducted in a group stigmatized because of beliefs that the disease is familial. Podoconiosis, also known as 'mossy foot', is an example of such a disease. It is a condition resulting in swelling of the lower legs among people exposed to red clay soil. It is a very stigmatizing problem in endemic areas of Ethiopia because of the widely held opinion that the disease runs in families and is untreatable. The aim of this study was to explore the impact of social stigma on the process of obtaining consent for a study on the genetics of podoconiosis in Southern Ethiopia.

Methods

We adapted a rapid assessment tool validated in The Gambia. The methodology was qualitative involving focus-group discussions (n = 4) and in-depth interviews (n = 25) with community members, fieldworkers, researchers and staff of the Mossy Foot Treatment and Prevention Association (MFTPA) working on prevention and treatment of podoconiosis.

Results

We found that patients were afraid of participation in a genetic study for fear the study might aggravate stigmatization by publicizing the familial nature of the disease. The MFTPA was also concerned that discussion about the familial nature of podoconiosis would disappoint patients and would threaten the trust they have in the organization. In addition, participants of the rapid assessment stressed that the genetic study should be approved at family level before prospective participants are approached for consent. Based on this feedback, we developed and implemented a consent process involving community consensus and education of fieldworkers, community members and health workers. In addition, we utilized the experience and established trust of the MFTPA to diminish the perceived risk.

Conclusion

The study showed that the consent process developed based on issues highlighted in the rapid assessment facilitated recruitment of participants and increased their confidence that the genetic research would not fuel stigma. Therefore, investigators must seek to assess and address risks of research from prospective participants' perspectives. This involves understanding the issues in the society, the culture, community dialogues and developing a consent process that takes all these into consideration.

Background

Although age-related loss of fat free mass (FFM) is well known, there is paucity of data on national estimates, and on the differential influence of ethnicity on the decline in FFM with increasing age. We determined whether age-related loss in FFM and fat free mass index (FFMI) vary by gender and or ethnicity, using representative data from the Third National Health and Nutrition Examination Survey (NHANES III).

Methods

Analyses were limited to 5,803 non-institutionalized, non-Hispanic Whites and African Americans (Blacks) over the age of 40 years. Body density was calculated from the sum of 3-skinfolds, and percent body fat estimated from body density. FFM was estimated by subtracting body fat from body weight, while FFMI was defined as FFM (kilograms) divided by the square of body height (meter2).

Results

Overall FFM and FFMI were significantly higher in black women than white women (P = 0.001; P = 0.001 respectively), but similar in black men compared to white men. Age-related decline in FFM reached significance level earlier in black men (at age 65–69) than white men (at age 70–74), and in black women (at age 70–74) than white women (at age 75–79). Similar decline in FFMI was noted in men and in women. In multivariate analyses, FFM significantly associated with ethnicity (p = 0.012) and with age (p < 0.001) in women, but only with age (p < 0.001) in men. In men and in women, FFMI significantly associated with ethnicity (p < 0.001; p = 0.003 respectively) and with age (p < 0.001; p = 0.004 respectively).

Conclusion

Age-related loss and decline in FFM and FFMI in older Americans is higher for black men and women, than for white men and women. The development of focused population-based preventive strategies is likely to improve functional independence in the aged.

Objective

To determine the correlates of serum lipoprotein (a) (Lp(a)) in children and adolescents in the United States.

Methods

Cross-sectional study using representative data from a US national sample for persons aged 4–19 years participating in The Third National Health Nutrition and Examination Survey (NHANES-III).

Results

We observed ethnicity-related differences in levels of Lp(a) > 30 mg/dl, with values being markedly higher in African American (black) than nonhispanic white (white) and Mexican American children in multivariate model (P < 0.001). Higher levels of Lp(a) > 30 mg/dl associated with parental history of body mass index and residence in metro compared to nonmetro in Blacks, and high birth weight in Mexican American children in the NHANES-III. In the entire group, total cholesterol (which included Lp(a)) and parental history of premature heart attack/angina before age 50 (P < 0.02) showed consistent, independent, positive association with Lp(a). In subgroup analysis, this association was only evident in white (P = 0.04) and black (P = 0.05) children. However, no such collective consistent associations of Lp(a) were found with age, gender, or birth weight.

Conclusion

Ethnicity-related differences in mean Lp(a) exist among children and adolescents in the United States and parental history of premature heart attack/angina significantly associated with levels of Lp(a) in children. Further research on the associations of Lp(a) levels in childhood with subsequent risk of atherosclerosis is needed.

Background

The aim of this study was to examine the relationship between waist–hip ratio and the risk of breast cancer in an urban Nigerian population.

Methods

Between March 1998 and August 2000, we conducted a case–control study of hospital-based breast cancer patients (n = 234) and population-based controls (n = 273) using nurse interviewers in urban Southwestern Nigeria.

Results

Multivariable logistic regression showed a significant association between the highest tertile of waist–hip ratio and the risk of breast cancer (odds ratio= 2.67, 95% confidence interval = 1.05–6.80) among postmenopausal women. No association was found in premenopausal women.

Conclusion

The present study, the first in an indigenous African population, supports other studies that have shown a positive association between obesity and breast cancer risk among postmenopausal women.