Asthma originates from genetic and environmental factors with about half the risk of disease attributable to heritable causes. Genome-wide association studies, mostly in populations of European ancestry, have identified numerous asthma-associated single nucleotide polymorphisms (SNPs). Studies in populations with diverse ancestries allow both for identification of robust associations that replicate across ethnic groups and for improved resolution of associated loci due to different patterns of linkage disequilibrium between ethnic groups. Here we report on an analysis of 745 African-American subjects with asthma and 3,238 African-American control subjects from the Candidate Gene Association Resource (CARe) Consortium, including analysis of SNPs imputed using 1,000 Genomes reference panels and adjustment for local ancestry. We show strong evidence that variation near RAD50/IL13, implicated in studies of European ancestry individuals, replicates in individuals largely of African ancestry. Fine mapping in African ancestry populations also refined the variants of interest for this association. We also provide strong or nominal evidence of replication at loci near ORMDL3/GSDMB, IL1RL1/IL18R1, and 10p14, all previously associated with asthma in European or Japanese populations, but not at the PYHIN1 locus previously reported in studies of African-American samples. These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry.

Keri Monda, Kari North, Christopher Haiman and colleagues report a meta-analysis of GWAS for body mass index that is composed of 39,144 individuals of African ancestry, followed by further genotyping in 32,268 individuals of African ancestry. The study also includes analysis of publicly available data from the GIANT consortium of ~124,000 individuals of European ancestry. The paper reports evidence for two new loci near GALNT10 and MIR148A. Genome-wide association studies (GWAS) have identified 36 loci associated with body mass index (BMI), predominantly in populations of European ancestry. We conducted a meta-analysis to examine the association of >3.2 million SNPs with BMI in 39,144 men and women of African ancestry and followed up the most significant associations in an additional 32,268 individuals of African ancestry. We identified one new locus at 5q33 (GALNT10, rs7708584, P = 3.4 × 10−11) and another at 7p15 when we included data from the GIANT consortium (MIR148A-NFE2L3, rs10261878, P = 1.2 × 10−10). We also found suggestive evidence of an association at a third locus at 6q16 in the African-ancestry sample (KLHL32, rs974417, P = 6.9 × 10−8). Thirty-two of the 36 previously established BMI variants showed directionally consistent effect estimates in our GWAS (binomial P = 9.7 × 10−7), five of which reached genome-wide significance. These findings provide strong support for shared BMI loci across populations, as well as for the utility of studying ancestrally diverse populations.

[This corrects the article DOI: 10.1371/journal.pone.0044008.].

Background: Thymic stromal lymphopoietin (TSLP), an IL7-like cytokine produced by bronchial epithelial cells is upregulated in asthma and induces dendritic cell maturation supporting a Th2 response. Environmental pollutants, including tobacco smoke and diesel exhaust particles upregulate TSLP suggesting that TSLP may be an interface between environmental pollution and immune responses in asthma. Since asthma is prevalent in urban communities, variants in the TSLP gene may be important in asthma susceptibility in these populations.Objectives: To determine whether genetic variants in TSLP are associated with asthma in an urban admixed population.Methodology and Main Results: Ten tag-SNPs in the TSLP gene were analyzed for association with asthma using 387 clinically diagnosed asthmatic cases and 212 healthy controls from an urban admixed population. One SNP (rs1898671) showed nominally significant association with asthma (odds ratio (OR) = 1.50; 95% confidence interval (95% CI): 1.09-2.05, p = 0.01) after adjusting for age, BMI, income, education and population stratification. Association results were consistent using two different approaches to adjust for population stratification. When stratified by smoking status, the same SNP showed a significantly increased risk associated with asthma in ex-smokers (OR = 2.00, 95% CI: 1.04-3.83, p = 0.04) but not significant in never-smokers (OR = 1.34; 95% CI: 0.93-1.94, p = 0.11). Haplotype-specific score test indicated that an elevated risk for asthma was associated with a specific haplotype of TSLP involving SNP rs1898671 (OR = 1.58, 95% CI: 1.10-2.27, p = 0.01). Association of this SNP with asthma was confirmed in an independent large population-based cohort consortium study (OR = 1.15, 95% CI: 1.07-1.23, p = 0.0003) and the results stratified by smoking status were also validated (ex-smokers: OR = 1.21, 95% CI: 1.08-1.34, p = 0.003; never-smokers: OR = 1.06, 95% CI: 0.94-1.17, p = 0.33).Conclusions: Genetic variants in TSLP may contribute to asthma susceptibility in admixed urban populations with a gene and environment interaction.

Variation in the peroxisome proliferator–activated receptor γ gene alters the risk for adiposity in adults, with evidence of interaction with diet. We investigated the age-related association between the Pro12Ala variant (rs1801282) and diet in obesity-related traits in children. The Pro12Ala variant was assayed in 2102 young children aged 1 to 6 years and in 794 periadolescent children aged 10 to 12 years of Greek origin. In both cohorts, no differences were found in obesity traits between the Ala allele carriers and Pro/Pro homozygotes. Sex-stratified analysis showed that, in periadolescent boys, Ala carriers exhibited lower measures of skinfolds (triceps: 16.9 ± 6.9 vs 19.4 ± 7.9 mm, P = .01; subscapular: 9.6 ± 4.5 vs 11.2 ± 5.4 mm, P = .02). On the other hand, young girls who were Ala carriers presented higher measures of triceps skinfold thickness (10.5 ± 3.0 vs 9.9 ± 2.8 mm, P = .04). Nominal gene-diet interactions were revealed in periadolescents for saturated fatty acid (SFA) intake and skinfolds (P for interaction = .05). In Pro/Pro homozygous young girls, SFA and total fat (TF) intake was positively associated with higher body mass index (BMI) (P = .01), waist circumference (P = .02), and skinfold thickness (triceps-SFA: P = 10−5, triceps-TF: P = 10−9, subscapular-SFA: P = 10−6, subscapular-TF: P = 10−4). For Pro/Pro homozygotes, unsaturated fat intake was inversely associated with BMI (P = .04) in young girls, and with BMI (P = .03), waist circumference (P = .03), and triceps (P = .02) in periadolescent boys. Our results suggest that adiposity in children is influenced by the Pro12Ala polymorphism in a sex-specific and age-dependent manner. We also demonstrate evidence of an age-dependent gene-diet (SFA, TF) interaction, suggesting that the type of fat intake modifies the effect of the Pro12 allele on obesity-related measures.

ObjectiveTo determine whether maternal genetic variants modify the effect of exclusive breastfeeding (EBF) on postpartum weight retention.Study DesignIn a cohort of pregnant women we genotyped 248 self-identified Caucasian participants for 27 single-nucleotide polymorphisms (SNPs) associated with diabetes and obesity. We used linear regression to model the effect of genotype and interactions between genotype and EBF duration on retained weight at 3 and 12 months postpartum. All models were adjusted for pregravid BMI. Hierarchical selection was used to model quadratic and linear interactions between SNP carriage and EBF duration. P values <0.05 and interaction p values < 0.10 were considered statistically significant.ResultsThe average duration of EBF was 3.2 (SD 2.2) months. In models adjusting for pregravid BMI and gestational weight gain, duration of EBF was inversely associated with retained weight at 3 months (-1.3, 95% CI -2.1 to -0.5 lbs/month EBF) and at 12 months (-0.8, 95%CI -1.4 to -0.2 lbs/month EBF). At 3 months, we found a quadratic interaction between the diabetes-associated risk variant TCF7L2, EBF duration and retained weight. At 12 months, we found linear interactions between the diabetes-associated risk variants TCF2, JAZF1, and G6PC2, EBF duration, and retained weight (Figure). With further adjustment for gestational weight gain, for retained weight at 3 months, we found a quadratic interaction between TCF7L2 and EBF duration and a linear interaction between the variants SH2B1, INSIG2 and EBF duration. For retained weight at 12 months, we found linear interactions between JAZF1 and EBF duration.ConclusionsOur results provide tentative evidence that diabetes risk alleles may modify the effect of exclusive breastfeeding on maternal weight retention, but validation is needed in larger samples. ObjectiveTo determine whether maternal genetic variants modify the effect of exclusive breastfeeding (EBF) on postpartum weight retention. To determine whether maternal genetic variants modify the effect of exclusive breastfeeding (EBF) on postpartum weight retention. Study DesignIn a cohort of pregnant women we genotyped 248 self-identified Caucasian participants for 27 single-nucleotide polymorphisms (SNPs) associated with diabetes and obesity. We used linear regression to model the effect of genotype and interactions between genotype and EBF duration on retained weight at 3 and 12 months postpartum. All models were adjusted for pregravid BMI. Hierarchical selection was used to model quadratic and linear interactions between SNP carriage and EBF duration. P values <0.05 and interaction p values < 0.10 were considered statistically significant. In a cohort of pregnant women we genotyped 248 self-identified Caucasian participants for 27 single-nucleotide polymorphisms (SNPs) associated with diabetes and obesity. We used linear regression to model the effect of genotype and interactions between genotype and EBF duration on retained weight at 3 and 12 months postpartum. All models were adjusted for pregravid BMI. Hierarchical selection was used to model quadratic and linear interactions between SNP carriage and EBF duration. P values <0.05 and interaction p values < 0.10 were considered statistically significant. ResultsThe average duration of EBF was 3.2 (SD 2.2) months. In models adjusting for pregravid BMI and gestational weight gain, duration of EBF was inversely associated with retained weight at 3 months (-1.3, 95% CI -2.1 to -0.5 lbs/month EBF) and at 12 months (-0.8, 95%CI -1.4 to -0.2 lbs/month EBF). At 3 months, we found a quadratic interaction between the diabetes-associated risk variant TCF7L2, EBF duration and retained weight. At 12 months, we found linear interactions between the diabetes-associated risk variants TCF2, JAZF1, and G6PC2, EBF duration, and retained weight (Figure). With further adjustment for gestational weight gain, for retained weight at 3 months, we found a quadratic interaction between TCF7L2 and EBF duration and a linear interaction between the variants SH2B1, INSIG2 and EBF duration. For retained weight at 12 months, we found linear interactions between JAZF1 and EBF duration. The average duration of EBF was 3.2 (SD 2.2) months. In models adjusting for pregravid BMI and gestational weight gain, duration of EBF was inversely associated with retained weight at 3 months (-1.3, 95% CI -2.1 to -0.5 lbs/month EBF) and at 12 months (-0.8, 95%CI -1.4 to -0.2 lbs/month EBF). At 3 months, we found a quadratic interaction between the diabetes-associated risk variant TCF7L2, EBF duration and retained weight. At 12 months, we found linear interactions between the diabetes-associated risk variants TCF2, JAZF1, and G6PC2, EBF duration, and retained weight (Figure). With further adjustment for gestational weight gain, for retained weight at 3 months, we found a quadratic interaction between TCF7L2 and EBF duration and a linear interaction between the variants SH2B1, INSIG2 and EBF duration. For retained weight at 12 months, we found linear interactions between JAZF1 and EBF duration. ConclusionsOur results provide tentative evidence that diabetes risk alleles may modify the effect of exclusive breastfeeding on maternal weight retention, but validation is needed in larger samples. Our results provide tentative evidence that diabetes risk alleles may modify the effect of exclusive breastfeeding on maternal weight retention, but validation is needed in larger samples.

The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity.

Context. A number of studies have reported replicable associations between common genetic loci and obesity indices. One of these loci is the fat mass and obesity associated locus (FTO). We aimed to assess whether breastfeeding mediated the known association between FTO and indices of body fatness. Methods. This study includes three independent pediatric cohorts, two of Greek origin (the Gene-Diet Attica Investigation: GENDAI, n = 1 138 and the "Growth, Exercise and Nutrition Epidemiological Study In preschoolers": the GENESIS study, n = 2 374) and one British (the Avon Longitudinal Study of Parents and Children: ALSPAC, n = 4 325). Among other information, breastfeeding history was recorded. A DNA sample was ascertained by either blood or saliva. Genotyping for FTO variants was performed in GENDAI and ALSPAC for the rs9939609, while in GENESIS, for the rs17817449 variant. Results. In all cohorts, multivariate analysis showed that the association between FTO : rs9939609 and measures of obesity was consistent across newly presented cohorts (GENDAI: Body mass index [BMI], beta = 0.43, p = 0.009; Waist Circumference, beta = 1.067, p = 0.019; triceps skinfold, beta = 0.972, p = 0.003; subscapular skinfold, beta = 0.593, p = 0.023; GENESIS: Waist Circumference, beta = 0.473, p = 0.008 and subscapular skinfold, beta = 0.227, p = 0.014). Inclusion of one month of breastfeeding as an interaction term effectively removed these associations with indices of obesity (BMI, Waist-Hip-Ratio and subscapular skinfold). No evidence of such interaction was observed for the independent cohort of British children. Conclusions. Our findings indicate that in two moderately sized Greek samples, breastfeeding may exert a modifying effect on the relationship between variants at the FTO locus and indices of adiposity. These findings were not replicated in a larger British collection.

Genome-wide genotyping of a cohort using pools rather than individual samples has long been proposed as a cost-saving alternative for performing genome-wide association (GWA) studies. However, successful disease gene mapping using pooled genotyping has thus far been limited to detecting common variants with large effect sizes, which tend not to exist for many complex common diseases or traits. Therefore, for DNA pooling to be a viable strategy for conducting GWA studies, it is important to determine whether commonly used genome-wide SNP array platforms such as the Affymetrix 6.0 array can reliably detect common variants of small effect sizes using pooled DNA. Taking obesity and age at menarche as examples of human complex traits, we assessed the feasibility of genome-wide genotyping of pooled DNA as a single-stage design for phenotype association. By individually genotyping the top associations identified by pooling, we obtained a 14- to 16-fold enrichment of SNPs nominally associated with the phenotype, but we likely missed the top true associations. In addition, we assessed whether genotyping pooled DNA can serve as an inexpensive screen as the second stage of a multi-stage design with a large number of samples by comparing the most cost-effective 3-stage designs with 80% power to detect common variants with genotypic relative risk of 1.1, with and without pooling. Given the current state of the specific technology we employed and the associated genotyping costs, we showed through simulation that a design involving pooling would be 1.07 times more expensive than a design without pooling. Thus, while a significant amount of information exists within the data from pooled DNA, our analysis does not support genotyping pooled DNA as a means to efficiently identify common variants contributing small effects to phenotypes of interest. While our conclusions were based on the specific technology and study design we employed, the approach presented here will be useful for evaluating the utility of other or future genome-wide genotyping platforms in pooled DNA studies.

To determine whether maternal genetic variants are associated with postpartum weight retention. In a cohort study of pregnant women, we genotyped 267 self-identified Caucasian participants for 27 single-nucleotide polymorphisms (SNPs) associated with diabetes and obesity. We used Linear regression to model the effect of genotype on retained weight at 3 and 12 months postpartum. All models were adjusted for pregravid BMI. P values of <0.05 were considered statistically significant. Our study population included 267 women with a mean pregravid BMI of 24.5 (SD 6.2) kg/m2. Mean retained weight at 3 and 12 months was 9.1 (SD 10.7) and 4.7 (SD 12.1) lbs, respectively. Compared with women with 0 copies of the risk allele, we found greater weight retention at 3 months among women homozygous for the TCF2 risks allele (4.1 lbs, 95% 0.5, 7.7lbs) and among women heterozygous for the INSIG2 and NEGR1 risk alleles (3.1 lbs, 95% CI 0.3, 5.9 and 3.3 lbs, 95% CI 0.0, 6.7). We found reduced weight retention among women with one or two copies of the KCNJ11 risk allele (1 allele: -2.9 lbs, 95% CI -5.6, -0.2; 2 alleles: -5.2, 95% CI -9.5, -0.9), with one copy of the WFS1 risk allele (-3.3 lbs, 95% CI -6.1, -0.4), and with two copies of the TCF7L2 risk allele (-6.1, 95% CI -11.2,-0.9), compared with 0 alleles. At 12 months postpartum (N=208), we found reduced weight retention among women with two copies of the KCNJ11 risk allele (-6.9, 95% CI -12.2,-1.7). Our results provide tentative evidence that diabetes and obesity risk alleles may affect maternal weight retention, but validation is needed in larger samples.

To identify genetic variants associated with birth weight, we meta-analyzed six genome-wide association (GWA) studies (n = 10,623 Europeans from pregnancy/birth cohorts) and followed up two lead signals in 13 replication studies (n = 27,591). rs900400 near LEKR1 and CCNL1 (P = 2 x 10(-35)) and rs9883204 in ADCY5 (P = 7 x 10(-15)) were robustly associated with birth weight. Correlated SNPs in ADCY5 were recently implicated in regulation of glucose levels and susceptibility to type 2 diabetes, providing evidence that the well-described association between lower birth weight and subsequent type 2 diabetes has a genetic component, distinct from the proposed role of programming by maternal nutrition. Using data from both SNPs, we found that the 9% of Europeans carrying four birth weight-lowering alleles were, on average, 113 g (95% CI 89-137 g) lighter at birth than the 24% with zero or one alleles (P(trend) = 7 x 10(-30)). The impact on birth weight is similar to that of a mother smoking 4-5 cigarettes per day in the third trimester of pregnancy.

OBJECTIVE:We sought to determine whether genetic variants associated with diabetes and obesity predict gestational weight gain. STUDY DESIGN:A total of 960 participants in the Pregnancy, Infection, and Nutrition cohorts were genotyped for 27 single-nucleotide polymorphisms (SNPs) associated with diabetes and obesity. RESULTS:Among Caucasian and African American women (n = 960), KCNQ1 risk allele carriage was directly associated with weight gain (P < .01). In Bayesian hierarchical models among Caucasian women (n = 628), we found posterior odds ratios >3 for inclusion of TCF2 and THADA SNPs in our models. Among African American women (n = 332), we found associations between risk allele carriage and weight gain for the THADA and INSIG2 SNPs. In Bayesian variable selection models, we found an interaction between the TSPAN8 risk allele and pregravid obesity, with lower weight gain among obese risk allele carriers. CONCLUSION:We found evidence that diabetes and obesity risk alleles interact with maternal pregravid body mass index to predict gestational weight gain.

MOTIVATION:Adjustment for population structure is necessary to avoid bias in genetic association studies of susceptibility variants for complex diseases. Population structure may differ from one genomic region to another due to the variability of individual ancestry associated with migration, random genetic drift or natural selection. Current association methods for correcting population stratification usually involve adjustment of global ancestry between study subjects. RESULTS:We suggest interrogating local population structure for fine mapping to more accurately locate true casual genes by better adjusting the confounding effect due to local ancestry. By extensive simulations on genome-wide datasets, we show that adjusting global ancestry may lead to false positives when local population structure is an important confounding factor. In contrast, adjusting local ancestry can effectively prevent false positives due to local population structure and thus can improve fine mapping for disease gene localization. We applied the local and global adjustments to the analysis of datasets from three genome-wide association studies, including European Americans, African Americans and Nigerians. Both European Americans and African Americans demonstrate greater variability in local ancestry than Nigerians. Adjusting local ancestry successfully eliminated the known spurious association between SNPs in the LCT gene and height due to the population structure existed in European Americans. CONTACT:xiaofeng.zhu@case.edu SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

Genome-wide association studies have identified many common genetic variants that are associated with polygenic traits, and have typically been performed with individuals of recent European ancestry. In these populations, many common variants are tightly correlated, with the perfect or near-perfect proxies for the functional or true variant showing equivalent evidence of association, considerably limiting the resolution of fine mapping. Populations with recent African ancestry often have less extensive and/or different patterns of linkage disequilibrium (LD), and have been proposed to be useful in fine-mapping studies. Here, we strongly replicate and fine map in populations of predominantly African ancestry the association between variation at the FTO locus and body mass index (BMI) that is well established in populations of European ancestry. We genotyped single nucleotide polymorphisms that are correlated with the signal of association in individuals of European ancestry but that have varying degrees of correlation in African-derived individuals. Most of the variants, including one previously proposed as functionally important, have no significant association with BMI, but two variants, rs3751812 and rs9941349, show strong evidence of association (P = 2.58 x 10(-6) and 3.61 x 10(-6) in a meta-analysis of 9881 individuals). Thus, we have both strongly replicated this association in African-ancestry populations and narrowed the list of potentially causal variants to those that are correlated with rs3751812 and rs9941349 in African-derived populations. This study illustrates the potential of using populations with different LD patterns to fine map associations and helps pave the way for genetically guided functional studies at the FTO locus.

As we move forward from the current generation of genome-wide association (GWA) studies, additional cohorts of different ancestries will be studied to increase power, fine map association signals, and generalize association results to additional populations. Knowledge of genetic ancestry as well as population substructure will become increasingly important for GWA studies in populations of unknown ancestry. Here we propose genotyping pooled DNA samples using genome-wide SNP arrays as a viable option to efficiently and inexpensively estimate admixture proportion and identify ancestry informative markers (AIMs) in populations of unknown origin. We constructed DNA pools from African American, Native Hawaiian, Latina, and Jamaican samples and genotyped them using the Affymetrix 6.0 array. Aided by individual genotype data from the African American cohort, we established quality control filters to remove poorly performing SNPs and estimated allele frequencies for the remaining SNPs in each panel. We then applied a regression-based method to estimate the proportion of admixture in each cohort using the allele frequencies estimated from pooling and populations from the International HapMap Consortium as reference panels, and identified AIMs unique to each population. In this study, we demonstrated that genotyping pooled DNA samples yields estimates of admixture proportion that are both consistent with our knowledge of population history and similar to those obtained by genotyping known AIMs. Furthermore, through validation by individual genotyping, we demonstrated that pooling is quite effective for identifying SNPs with large allele frequency differences (i.e., AIMs) and that these AIMs are able to differentiate two closely related populations (HapMap JPT and CHB).

Genome-wide association (GWA) studies have identified common variants that are associated with a variety of traits and diseases, but most studies have been performed in European-derived populations. Here, we describe the first genome-wide analyses of imputed genotype and copy number variants (CNVs) for anthropometric measures in African-derived populations: 1188 Nigerians from Igbo-Ora and Ibadan, Nigeria, and 743 African-Americans from Maywood, IL. To improve the reach of our study, we used imputation to estimate genotypes at approximately 2.1 million single-nucleotide polymorphisms (SNPs) and also tested CNVs for association. No SNPs or common CNVs reached a genome-wide significance level for association with height or body mass index (BMI), and the best signals from a meta-analysis of the two cohorts did not replicate in approximately 3700 African-Americans and Jamaicans. However, several loci previously confirmed in European populations showed evidence of replication in our GWA panel of African-derived populations, including variants near IHH and DLEU7 for height and MC4R for BMI. Analysis of global burden of rare CNVs suggested that lean individuals possess greater total burden of CNVs, but this finding was not supported in an independent European population. Our results suggest that there are not multiple loci with strong effects on anthropometric traits in African-derived populations and that sample sizes comparable to those needed in European GWA studies will be required to identify replicable associations. Meta-analysis of this data set with additional studies in African-ancestry populations will be helpful to improve power to detect novel associations.