Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X

The prevalence of obesity (body mass index (BMI) ≥30 kg/m2) is higher in African Americans than in European Americans, even after adjustment for socioeconomic factors, suggesting that genetic factors may explain some of the difference. To identify genetic loci influencing BMI, we carried out a pooled analysis of genome-wide admixture mapping scans in 15,280 African Americans from 14 epidemiologic studies. Samples were genotyped at a median of 1,411 ancestry-informative markers. After adjusting for age, sex, and study, BMI was analyzed both as a dichotomized (top 20% versus bottom 20%) and a continuous trait. We found that a higher percentage of European ancestry was significantly correlated with lower BMI (ρ = −0.042, P = 1.6×10−7). In the dichotomized analysis, we detected two loci on chromosome X as associated with increased African ancestry: the first at Xq25 (locus-specific LOD = 5.94; genome-wide score = 3.22; case-control Z = −3.94); and the second at Xq13.1 (locus-specific LOD = 2.22; case-control Z = −4.62). Quantitative analysis identified a third locus at 5q13.3 where higher BMI was highly significantly associated with greater European ancestry (locus-specific LOD = 6.27; genome-wide score = 3.46). Further mapping studies with dense sets of markers will be necessary to identify the alleles in these regions of chromosomes X and 5 that may be associated with variation in BMI

Meta-analysis of genome-wide association studies identifies six new Loci for serum calcium concentrations.

Calcium is vital to the normal functioning of multiple organ systems and its serum concentration is tightly regulated. Apart from CASR, the genes associated with serum calcium are largely unknown. We conducted a genome-wide association meta-analysis of 39,400 individuals from 17 population-based cohorts and investigated the 14 most strongly associated loci in ≤ 21,679 additional individuals. Seven loci (six new regions) in association with serum calcium were identified and replicated. Rs1570669 near CYP24A1 (P = 9.1E-12), rs10491003 upstream of GATA3 (P = 4.8E-09) and rs7481584 in CARS (P = 1.2E-10) implicate regions involved in Mendelian calcemic disorders: Rs1550532 in DGKD (P = 8.2E-11), also associated with bone density, and rs7336933 near DGKH/KIAA0564 (P = 9.1E-10) are near genes that encode distinct isoforms of diacylglycerol kinase. Rs780094 is in GCKR. We characterized the expression of these genes in gut, kidney, and bone, and demonstrate modulation of gene expression in bone in response to dietary calcium in mice. Our results shed new light on the genetics of calcium homeostasis

Relative mRNA expression of identified genes from mice fed a low (0.17%) and high (1.69%) calcium diet compared to mice fed a normal calcium diet (0.82%).

<p>Data are means± SEM of values obtained from 5 mice for each diet group. Expression levels were normalized to actin. Statistical significance of the difference between diets was calculated using unpaired t-test. *: <i>P</i>≤0.05 (low compared to high); §: <i>P</i>≤0.05 (low compared to normal); # <i>P</i>≤0.05 (high compared to normal).</p

Genome-wide association for serum calcium in discovery analysis in Europeans.

<p>Manhattan plot showing −log₁₀(P values) for all SNPs in the discovery GWAS for uncorrected serum calcium in Europeans (N = 39,400), ordered by chromosomal position. The plot is truncated at −log10 P values of 10 (truncated −log₁₀P values for GCKR and CASR). The values correspond to the association of uncorrected serum calcium, including age and sex as covariates in the model as well as study-specific covariates if needed. The gene closest to the SNP with the lowest P value is listed at each locus. Six loci reached genome-wide significance (<i>P</i><5E-08) at discovery analysis (<i>GCKR</i>, <i>DGKD</i>, <i>CASR</i>, <i>VKORC1L1</i> (in grey on chromosome 7), <i>CARS</i> and <i>CYP24A1</i>. The seven loci that reached genome-wide significance at the combined analysis following replication are highlighted in red (<i>GCKR</i>, <i>DGKD</i>, CASR, <i>GATA3</i>, <i>CARS</i>, <i>DGKH</i>-KIAA0564 and <i>CYP24A1</i>).</p

Relative mRNA expression of replicated genes in three calcium-transporting tissues (kidney, duodenum, tibia).

<p>The expression (based on delta CT [cycle threshold] normalized to actin) of the selected genes is compared to the expression of the <i>CASR</i> gene in the duodenum, thereby providing a relative expression. Cut-off was set at delta CT≤15. Data are means ± standard error of the mean (SEM) of values obtained from 5 mice fed a normal diet. <i>GCKR</i> was not expressed.</p

Look-ups of serum calcium loci with related phenotypes: bone mineral density in the GEFOS dataset [6] and endocrine phenotypes from the SHIP, SHIP Trend and SUNLIGHT [7] datasets.

<p>NA, not available. P values<0.05 were considered as statistically significant. A1, effect allele. β, regression coefficient for allele A1, SE, standard error. P, two-sided P value. Zscore, z score.</p

Relative mRNA expression of identified genes in kidney tubule segments.

<p>The renal tubular segments analyzed were the proximal tubule (PROX), the thick ascending limb of the loop of Henle (TAL), the distal convoluted tubule and connecting tubule (DCT-CNT), and the cortical collecting duct (CCD). The expression (based on the delta CT [cycle threshold]) of the selected genes is compared to the expression of the <i>CASR</i> gene in the PROX, thereby providing a relative expression. Data are means of values obtained from 3 mice fed a normal diet. <i>GCKR</i> was not expressed.</p

Genome-wide significant and replicated loci for serum calcium in Europeans.

<p>P values are corrected for inflation using genomic control. Replication criteria: overall genome-wide significance (<i>P</i><5E-8) and one-sided replication <i>P</i><0.05. I² was zero for rs1801725, rs1550532, rs10491003, rs7336933 and rs1570669 (I²<i>P</i>>0.20). For rs780094 and rs7481584, I² were 0.79 and 0.43 with I²<i>P</i> 0.03 and 0.19, respectively. For these latter SNPs, sample size weighted meta-analysis P values were 2.93E-10 and 2.03E-10, respectively.</p><p>Chr, chromosome. Effect A1 = beta regression coefficient for allele A1; SE, standard error.</p>*<p>one-sided P values.</p