Test-statistic inflation in methylome-wide association studies

Figures & data

Figure 1. Effects of covariate inclusion on test-statistic inflation. quantile-quantile (QQ) plots for the outcomes postpartum depression case status (a) and age (b). Each colour denotes a different level of quality control used in association testing: no covariates (red), commonly used pipeline (green), and our proposed iterative quality control process (blue)

Table 1. GEO Datasets included in systematic review

GEO Accession	PMID	n	Platform	Tissue	Outcome	Initial Lambda	Recalculated Lambda	Permutation Median Lambda (95% CI)	Bonferroni Δ	Source of Initial Lambda
GSE56046	25404168	1202	450 k	Blood	age	3.12	-	-		MWAS of processed data
GSE87571	23826282	732	450 k	Blood	age	17.68	7.69	0.97 (0.86–1.38)	92,591	Calculated from summary statistics
GSE72774	26655927	508	450 k	Blood (all samples)	age	5.48	-	-		MWAS of processed data
				Blood (controls only)	age	2.16	-	-
GSE72778	27479945	475	450 k	Brain (meta-analysis)	age	7.30	-	-		Reported in manuscript
				Brain (frontal lobe)	age	3.50	-	-
				Brain (parietal lobe)	age	3.00	-	-
				Brain (occipital lobe)	age	2.20	-	-
GSE55763	25853392	2711	450 k	Blood	Case-control	1.00	-	-		Reported in manuscript
GSE84727	27572077	847	450 k	Blood	Case-control	1.53	-	-		MWAS of processed data
GSE42861	23334450	689	450 k	Blood	Case-control	15.17	1.14	1.00 (0.96–1.08)	57,805	MWAS of processed data
GSE74193	26619358	675	450 k	Brain	Case-control	64.65	4.37	0.98 (0.78–1.35)	178,241	Calculated from summary statistics
GSE80417	27572077	675	450 k	Blood	Case-control	1.32	-	-		MWAS of processed data
GSE111629	28851441	572	450 k	Blood	Case-control	1.77	1.01	1.00 (0.93–1.11)	7	MWAS of processed data
GSE87648	27886173	384	450 k	Blood	Case-control	1.54	1.13	1.01 (0.82–1.35)	−202	MWAS of processed data
GSE100264	29269866	386	450 k	Blood	Ordinal (drug use)	1.08	-	-		Reported in manuscript