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Table 1 GAW20 quality control and statistical models, data sets, and software used by this group

From: Epigenetics, heritability and longitudinal analysis

Contribution

Phenotype

Normalization

h2

Covariates

CpG probes

Model(s)

Software

Almeida et al. [22]

HDL

Inverse

Pre and post fenofibrate HDL and CpG sites

20 PCs

Epigenome-wide

VC-LME

SOLAR

Canty and Paterson [20]

TG, QC

Probe type strata

–

4 PCs

Difference in TGs

Epigenome-wide

Standard linear model (t-test)

 

Fernandez-Rhodes et al. [25]

Metabolic syndrome

Type II probes

Metabolic syndrome, 4 CpG sites

age, sex, SNPs, center, smoking, PCs

4 CpG sites

VC-LME

SOLAR

LeBlanc et al. [21]

QC only

BMIQ

Used breeding values from a heritability model

Age, sex, SNPs

Epigenome-wide

Bayesian LME

R-INLA

Lim et al. [23]

TG

BMIQ

 

Age, sex, study, center, smoking, 10 PCs

14,850 CpG sites showing

LME

WGCNA, missmethyl

Nustad et al. [24]

TG, HDL

BMIQ

P-to-e and post fenofibrate, TG HDL and CpG sites

Age, sex

Epigenome-wide

Bayesian LME

R-package INLA

Yu et al. [26]

TG

–

 

Age, sex, study center, smoking status, HDL

349,755 CpG sites

GEE

R 3.2

  1. All contributions in this group used the GAW20 real data set
  2. BMIQ beta-mixture quantile normalization method for correcting probe design bias, GEE generalized estimating equation, HDL high-density lipoprotein, h2 denotes heritability and indicates if the paper has estimated this quantity, INLA integrated nested Laplace approximation, PC DNA methylation-derived principal component and indicates this study employed PCs as covariates in their analysis, QC quality control, SOLAR sequential oligogenic linkage analysis routines, SNP single-nucleotide polymorphism, TG triglyceride, VC-LME variance component linear mixed effect, WGCNA weighted gene coexpression network analysis