Table 1. Primer sequences used for pyrosequencing. Table 2. Beta value thresholds used for DNA methylation arrays and pyrosequencing. Figure S1. Strategy used to identify contamination in male samples. Plotting PC2, which separated male from female samples in our data, against DNA methylation at a CpG in XIST on the X chromosome, revealed three populations of male samples: contaminated, non-contaminated, and a group of five samples which were unclear. Figure S2. Neither epigenetic age (A), gestational epigenetic age (B) nor number of genotyping “no calls” (C) were sufficient to identify maternal blood contamination of cord blood. In all cases, contaminated and non-contaminated males showed high overlap, indicating insufficient discrimination. Figure S3. Across-batch differences in DNA methylation level support the use of multiple predictive CpGs for identification of contamination. Residual plot of discovery data (A), validation data (B), publically-available data (C), and PREDO (D) indicate technical spread across samples and studies. In particular, EPIC data (second cohort, top right) shows greater variability and higher baseline levels than the 450K data sets. (PDF 759 kb
