Longitudinal data methods for evaluating genome-by-epigenome interactions in families

BMC Genomic Data

Table 1 Power and Type I error rates for gene by methylation interactions

Model	Outcome	Nominal (p < 0.05)						Genome-wide (p < 1.08 × 10^− 7)
Model	Outcome	1 (0.125)	8 (0.10)	6 (0.075)	17 (0.05)	10 (0.025)	Type I error	1 (0.125)	8 (0.10)	6 (0.075)	17 (0.05)	10 (0.025)	Type I error
LME	Pre/Post	0.930	0.790	0.690	0.545	0.290	0.048	0.016	0.020	0.000	0.000	0.000	0.000
LME	Change	0.839	0.715	0.595	0.510	0.210	0.038	0.011	0.005	0.000	0.000	0.000	0.000
GEE	Pre/Post	0.935	0.835	0.705	0.555	0.290	0.073	0.022	0.025	0.005	0.000	0.000	0.002
GEE	Change	0.855	0.735	0.565	0.535	0.240	0.069	0.016	0.005	0.000	0.000	0.000	0.001
GEE–BC	Pre/Post	0.914	0.835	0.630	0.530	0.265	0.051	0.011	0.015	0.000	0.000	0.000	0.001
GEE–BC	Change	0.828	0.715	0.540	0.500	0.210	0.052	0.011	0.005	0.000	0.000	0.000	0.001
QIF	Pre/Post	0.941	0.845	0.685	0.580	0.410	0.120	0.054	0.055	0.015	0.000	0.005	0.002
QIF	Change	0.860	0.735	0.575	0.580	0.345	0.111	0.048	0.015	0.000	0.000	0.000	0.002
QIF–BC	Pre/Post	0.882	0.760	0.520	0.460	0.205	0.043	0.005	0.010	0.000	0.000	0.000	0.000
QIF–BC	Change	0.780	0.670	0.450	0.450	0.180	0.042	0.005	0.005	0.000	0.000	0.000	0.000

BC, Bias-corrected methods; Change, post-pre change triglyceride score as the outcome; GEE, generalized estimating equations; LME, linear mixed effects; Pre/Post, posttreatment triglyceride as the outcome and pretreatment as a baseline covariate; QIF, quadratic inference functions
The proportion of 200 (or 186 in the case of the chromosome 1 site) replicates that each SNP × CpG interaction was identified as significant for each significance threshold. Presented is the chromosome location with simulated expected heritability (h_g²) in parentheses
Causal chromosome sites simulated include: Chr 1 (SNP: rs9661059; CpG: cg00000363); Chr 8 (SNP: rs1012116; CpG: cg18772399); Chr 6 (SNP: rs736004; CpG: cg10480950); Chr 17 (SNP: rs4399565; CpG: cg01242676); and Chr 10 (SNP: rs10828412; CpG: cg00045910)

ISSN: 2730-6844