Table 2.

 Characteristics of EWASs associated with glycaemic traits

Referencea	Population for DNA methylation analysis	Female/male	Design	Tissue	Method	Covariates included into analysis	Multiple-testing correctionb	Top findings	No. of CpGs included in replication studyc
Kriebel et al, 2016 [33] a	1448 non-diabetic individuals (fasting glucose, 2-h glucose, HbA1c); 1440 non-diabetic individuals (fasting insulin, HOMA-IR); 617 non-diabetic individuals (2-h insulin)	47.1% male	Cross-sectional	Blood	450k	FDR	Age, sex, cell count (Houseman method), smoking, BMI	Total of 31 CpGs were found to be associated with phenotypic traits: 5 DMS associated with fasting glucose (including ABCG1, CPT1A), 1 with 2-h glucose, 8 with fasting insulin, 26 with HOMA-IR and none with HbA1c. Using a different model, adjustment for BMI resulted in ~30% reduction in effect size, suggesting BMI had a confounding effect	3 for fasting glucose
Kulkarni et al, 2015 [25] a	850 pedigreed Mexican Americans (174 T2D patients)	536/314	Cross-sectional (case–control)	Blood	450k	Bonferroni	Age, sex, BMI, cell count (Jaffe method)	51 CpGs were significantly associated with T2D, 19 with fasting glucose and 24 with HOMA-IR	19 for fasting glucose
Hidalgo et al, 2014 [34]	544 healthy individuals in discovery stage, 293 in replication stage	286/258	Cross-sectional	Blood	450k	Bonferroni	Age, sex, study site, 4 PC, insulin, glucose	1 DMS associated with fasting insulin and HOMA-IR: ABCG1 (cg06500161); marginally significant site also in ABCG1 (cg1881899, p = 3.36 × 10−6), associated with HOMA-IR only. No DMS associated with fasting glucose	0 (no information about insulin levels in Lifelines)
Ronn et al, 2015 [35] a	96 healthy male participants for discovery stage, 94 healthy female participants for validation stage, 2 separate EWASs performed	96 male 94 female	Cross-sectional association with age, BMI and HbA1c	Adipose tissue	450k	FDR < 5%, q < 0.05	Sex, family number; pedigree, age, BMI	711 DMS associated with HbA1c were found in the male cohort with most significant negative correlation at ANKRD11 gene; 7 DMS associated with HbA1c were found in the female cohort, none of which were significantly associated with HbA1c level in the male cohort	11 from male cohort

^aStudies included into replication study to provide CpGs, which passed strict Bonferroni correction threshold

^bMultiple-testing threshold calculated originally by the authors of particular study

^c0 in last column means zero CpG sites passed study-specific Bonferroni correction threshold

C, controls; DMS, differentially methylated sites; DMR, differentially methylated region; FDR, false discovery rate; HOMA-IR, homeostatic model assessment; NASH, non-alcoholic steatohepatitis; P, patients; PC, principal component; T2D, type 2 diabetes; 27k, Infinium HumanMethylation27 BeadChip; 450k, Infinium HumanMethylation450 BeadChip