Blood cell composition

Blood cell counts were available for 477 individuals, where blood leukocyte subtypes (monocytes, lymphocytes, basophils, neutrophils, eosinophiles) were counted using a Coulter LH 750 Hematology Analyzer (Beckman Coulter, Woerden, The Netherlands). For the remaining nine individuals, where blood cell composition was not available, data was imputed by partial least squares regression. A regression model was first fitted based on the samples for which measurements were available, and afterwards the model was applied for prediction of missing cell counts. The model used log(cell count+1) as response and included all beta values, that were available for all samples, as covariates. Detailed procedure for cell imputation is provided on GitHub (https://github.com/mvaniterson/wbccPredictor). Further covariates included were gender, age at follow-up visit, and sentrix position (modeled by two categorical variables indicating the position in each of the two directions on the chip: Left or Right and respectively 1–6 for the other direction). All calculations were performed in R (R Core Team, 2015).