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Brief Report

Validation of a DNA methylation reference panel for the estimation of nucleated cells types in cord blood

, , , , , , & show all
Pages 773-779 | Received 18 Jul 2016, Accepted 31 Aug 2016, Published online: 01 Nov 2016
 

ABSTRACT

Cord blood is widely used as surrogate tissue in epigenome-wide association studies of prenatal conditions. Cell type composition variation across samples can be an important confounder of epigenome-wide association studies in blood that constitute a mixture of cells. We evaluated a newly developed cord blood reference panel to impute cell type composition from DNA methylation levels, including nucleated red blood cells (nRBCs). We estimated cell type composition from 154 unique cord blood samples with available DNA methylation data as well as direct measurements of nucleated cell types. We observed high correlations between the estimated and measured composition for nRBCs (r = 0.92, R2 = 0.85), lymphocytes (r = 0.77, R2 = 0.58), and granulocytes (r = 0.72, R2 = 0.52), and a moderate correlation for monocytes (r = 0.51, R2 = 0.25) as well as relatively low root mean square errors from the residuals ranging from 1.4 to 5.4%. These results validate the use of the cord blood reference panel and highlight its utility and limitations for epidemiological studies.

Disclosure of potential conflicts of interest

No potential conflicts of interest were disclosed.

Funding

Fonds de recherche du Québec en santé #20697 (M.-F.H.); Canadian Institute of Health Research #MOP 115071 (M.-F.H.); Diabéte Québec grant (P.P.); ADA Accelerator Award #1-15-ACE-26 (M.-F.H.).