A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

Table 1 Main Illumina 450k DNAm datasets used. We list the main datasets used in this study, the cell-types/tissue profiled, whether the data was used for reference database construction (if yes, we specify which cell-types were used), whether the data was used for validation/evaluation purposes (if yes, we specify which cell-types were used) and the reference/citation

Dataset Name	Tissue/cell-types	Use in Reference DNAm Database	Testing/Evaluation	Reference
Reinius et al.	WB, PBMC, NK, B, CD4T, CD8T, Monoc, Neutro, Eosino. (n = 6 of each)	NK, B, CD4T, CD8T, Monoc., Neutro., Eosino.	WB & PBMC	[24]
Liu et al.	WB (n = 335 controls, n = 354 rheumathoid arthritis cases)	No	Average Flow Cytometry estimates for cases and controls	[2]
Koestler et al.	WB (n = 18)	No	12 Reconstructed WB mixtures + 6 WB samples with Flow Cytometry estimates	[20]
Zilbauer et al.	PBMC, CD4T, CD8T, NK, B, Monoc, Neutro. (n = 6 of each)	No	In-silico mixtures of purified blood cell subtypes	[27]
ENCODE	Various	HMEC, HRCE, IMR90, Liver	No	[22]
Slieker et al.	Various	Pancreas	Liver	[26]
SCM2	Various	No	HRCE, Pancreas, IMR90	[29]
Lowe et al.	Various	No	HMEC	[28, 35]
Teschendorff et al.	WB (n = 152)	No	Smoking associated DMCs	[31]

Abbreviations: DNAm = DNA methylation, WB = whole blood, PBMC = peripheral blood mononuclear cells, HMEC = human mammary epithelial cells, HRCE = human renal cortical epithelia, IMR90 (fetal lung fibroblast), SCM2 = Stem-Cell-Matrix Compendium-2, DMCs = differentially methylated CpGs, NK = natural killer cells, B = B-cell, Monoc = Monocytes, Neutro. = Neutrophils, Eosino = Eosinophils, CD4T = CD4+ T-cells, CD8T = CD8+ T-cells

ISSN: 1471-2105