Methylome-wide Association Analysis
To create a multi-probe methylation predictor, we first conducted a methylome-wide association analysis. A total of 431,951 and 407,935 CpG probes remained in the LBC and LifeLines DEEP datasets, respectively, after QC and probe filtering. Probes with an association p value < 1.16 × 10−7 in the LBC dataset and a p value < 1.22 × 10−7 in the LifeLines DEEP dataset were considered to be significantly associated after Bonferroni correction for the number of probes tested. After removal of correlated probes, nine CpG probes in the LBC dataset and five probes in the LifeLines DEEP dataset were associated with BMI and were used for generating methylation-profile scores (Table S1). Two probes (cg06500161 and cg11024682) were significantly associated with BMI in both cohorts—cg06500161 is found in an intronic region of ABCG1 (ATP-binding cassette, sub-family G, member 1 [MIM: 603076]), and cg11024682 is intronic to one isoform of SREBF1 (sterol regulatory element binding transcription factor 1 [MIM: 184756]). Both genes are known to be involved in lipid metabolism, but neither has been identified by GWASs to harbor genetic variants that are associated with BMI.
For height, no CpG probes passed the p value threshold in the LBCs, whereas only a single probe passed the threshold in the LifeLines DEEP cohort. Therefore, to generate a height-profile score, we used a less stringent association p value of <0.001 for probe selection. 507 and 949 CpG probes were selected in the LBCs and LifeLines DEEP cohort, respectively. Quantile-quantile plots for each MWAS are shown in Figure S3. We observed inflation in the lambda values—for BMI, lambdas were 1.53 and 1.17 in the LBCs and LifeLines DEEP cohort, respectively, whereas for height, lambdas were 1.12 and 1.36, respectively. Lambdas close to 1 (SD = 0.1) were observed with permutation analysis (performed in both the LBCs and LifeLines DEEP cohort), which indicates that the inflation was due to real signal and not an artifact of our assumption of the null distribution of the test statistic.