EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children

Abstract

Common variations at the loci harboring the fat mass and obesity gene (FTO), MC4R, and TMEM18 are consistently reported as being associated with obesity and body mass index (BMI) especially in adult population. In order to confirm this effect in pediatric population five European ancestry cohorts from pediatric eMERGE-II network (CCHMC-BCH) were evaluated.

Method: Data on 5049 samples of European ancestry were obtained from the Electronic Medical Records (EMRs) of two large academic centers in five different genotyped cohorts. For all available samples, gender, age, height, and weight were collected and BMI was calculated. To account for age and sex differences in BMI, BMI z-scores were generated using 2000 Centers of Disease Control and Prevention (CDC) growth charts. A Genome-wide association study (GWAS) was performed with BMI z-score. After removing missing data and outliers based on principal components (PC) analyses, 2860 samples were used for the GWAS study. The association between each single nucleotide polymorphism (SNP) and BMI was tested using linear regression adjusting for age, gender, and PC by cohort. The effects of SNPs were modeled assuming additive, recessive, and dominant effects of the minor allele. Meta-analysis was conducted using a weighted z-score approach.

Results: The mean age of subjects was 9.8 years (range 2-19). The proportion of male subjects was 56%. In these cohorts, 14% of samples had a BMI ≥95 and 28 ≥ 85%. Meta analyses produced a signal at 16q12 genomic region with the best result of p = 1.43 × 10(-) (7) [p (rec) = 7.34 × 10(-) (8)) for the SNP rs8050136 at the first intron of FTO gene (z = 5.26) and with no heterogeneity between cohorts (p = 0.77). Under a recessive model, another published SNP at this locus, rs1421085, generates the best result [z = 5.782, p (rec) = 8.21 × 10(-) (9)]. Imputation in this region using dense 1000-Genome and Hapmap CEU samples revealed 71 SNPs with p < 10(-) (6), all at the first intron of FTO locus. When hetero-geneity was permitted between cohorts, signals were also obtained in other previously identified loci, including MC4R (rs12964056, p = 6.87 × 10(-) (7), z = -4.98), cholecystokinin CCK (rs8192472, p = 1.33 × 10(-) (6), z = -4.85), Interleukin 15 (rs2099884, p = 1.27 × 10(-) (5), z = 4.34), low density lipoprotein receptor-related protein 1B [LRP1B (rs7583748, p = 0.00013, z = -3.81)] and near transmembrane protein 18 (TMEM18) (rs7561317, p = 0.001, z = -3.17). We also detected a novel locus at chromosome 3 at COL6A5 [best SNP = rs1542829, minor allele frequency (MAF) of 5% p = 4.35 × 10(-) (9), z = 5.89].

Conclusion: An EMR linked cohort study demonstrates that the BMI-Z measurements can be successfully extracted and linked to genomic data with meaningful confirmatory results. We verified the high prevalence of childhood rate of overweight and obesity in our cohort (28%). In addition, our data indicate that genetic variants in the first intron of FTO, a known adult genetic risk factor for BMI, are also robustly associated with BMI in pediatric population.

Keywords: BMI; GWAS; obesity; polymorphism.

FIGURE 1

(A,B) Manhattan plot and Q–Q plot of SNP markers used for meta-analyses (genomic inflation, λ = 1.007).

FIGURE 2

Genotypic correlation of FTO-SNP rs8050136 with mean of BMI-z score. The result further divided by age above and less than 5 years old respectively. All BMI-z scores (-3 to +3, mean = 0) were transformed to positive value (+4, 1–7, mean = 4).

FIGURE 3

Post imputation results on selected regions. (A) Imputation results and signal at FTO locus contributing to BMI. SNPs are plotted by position in a 0.2 Mb window of chromosome 16 against association with BMI-z (-log10 P-value). The panel highlights the most significant SNP in a meta-analysis using an additive model. Estimated recombination rates (from HapMap) are plotted in cyan to reflect the local LD structure. The SNPs surrounding the most significant SNP (rs8050135), are color-coded to reflect their LD with this SNP (taken from pairwise r² values from the HapMap CEU database, www.hapmap.org). Regional plots were generated using LocusZoom (http://csg.sph.umich.edu/locuszoom). (B) Regression results at the FTO locus under recessive model, best marker = rs1421085, p(rec) = 8.21 × 10^-9. (C) Imputation results near the MC4R locus at chromosome 18, is shown. Best marker rs12964056, p = 6.87 × 10^-7, z = -4.98. (D) A new effect at the COL6A5 locus in chromosome 3. Best marker rs1542829 p = 4.35 × 10^-9, z = 5.889.