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Table 1 Paper, data used, and methods implemented for capturing genetic, epigenetic, and associations with phenotypes

From: The challenge of detecting genotype-by-methylation interaction: GAW20

No Paper Data used GAW20 simulations
Answers known
Methods Specific data and modeling Response variable
1 Daw et al Simulated YES GLM
Linear mixed models
Regression trees
Random forest
Simulated data (200 replications)
Simulated effect sites + noise
ave(log(TGpost))
ave.(log(TGpost)) − ave.(log(TGpre))
2 Fisher et al Real data N/A Mediation interaction model GWAS
EWAS
pairs with P1 < 10−3 and P2 < 0.05
The effect of change in methylation on change in TG differs by genotype
Power: simulation with 500 replications
logTGpost − logTGpre
3 Hu and Li Real data N/A Gaussian mixture-model clustering
Gaphunter a thresholding-based method
CpG × SNP (GW) multimodal CpG sites
Association of CpG identified with overlapping SNP
Association with nearby SNPs
Pretreatment CpG
Posttreatment CpG
4 Romanescu et al Real data N/A Regional-based test Single CpG association (CH11)
Regional SNP PC association (CH11)
Regional CpG PC association (CH11)
Regional SNP + regional CpG association (CH11)
ave(ln(TGpre))
5 Sun et al Both YES Adaptive W-test with 2000 repetitions to get Type I error In both analysis main and interaction associations
Simulation: candidate pairs and noise pairs
Real data: (CH11)
delta(TG%) = 1, if delta(TG%) > 30% = 1, otherwise 0
delta(TG%) = (TGpre − TGpost)/TGpre
6 Veenstra et al Real data N/A Lmekin of coxme, lm in R (1) SNP association + (2) CpG association
(1) + (2) + CpG × SNP
Ave(TG1 + TG2) baseline
HDL
7 Zhou and Lo Real data N/A Group LASSO-regression, kinship matrix, stability selection CpG association (GW)
SNP association (GW)
(1) + (2) + CpG × SNP (CH11)
Ave(TG)
  1. Abbreviations: CH11 chromosome 11, CpG cytosine-phosphate-guanine, EWAS epigenome-wide association study, GLM generalized linear model, GW genome-wide, GWAS genome-wide association study, HDL high-density lipoprotein cholesterol, PC principal components; pre, pretreatment; post, posttreatment, SNP single-nucleotide polymorphism, TG triglyceride