Table 2.

Mean R² using the twofold and threefold cross-validation methods.

	2-fold cross-validation			3-fold cross-validation
Tissue pair	All CpGs	Removed CpGs with min methylation beta values >0.9 or max beta values <0.1	Removed CpGs with min methylation beta values >0.8 or max beta values <0.2	All CpGs	Removed CpGs with min methylation beta values >0.9 or max beta values <0.1	Removed CpGs with min methylation beta values >0.8 or max beta values <0.2
measured Placenta-measured Cord Blood	0.6567879	0.6333165	0.5079859	0.6567879	0.6333165	0.5079859
measured Placenta- SVM predicted Placenta	0.9672072	0.9644117	0.9472045	0.9676109	0.9648506	0.9478592

For the ‘All CpGs’ column, we used all CpG sites in each sample to calculate the CpG-wise R², and then obtained the mean R². For the ‘Removed CpGs with min methylation beta values>0.9 or max beta values<0.1’ column, we excluded the extreme CpGs that fell within this range and used the remaining data to calculate the mean CpG-wise R², and this column is similar to the ‘Removed CpGs with min methylation beta values>0.8 or max beta values<0.2’ column. For the ‘measured Placenta-measured Cord Blood’ row, the R² is the squared correlation coefficient of measured methylation in both placenta and cord blood. For the ‘measured Placenta-SVM predicted Placenta’ row, the R² is the squared correlation coefficient of measured methylation in the placenta and predicted methylation in the placenta by single-CpG-based SVM.