Fig. 4.

Pre-screening using the pyrosequencing method correctly identified contaminated male samples. a Applying a cut-off of 2 CpGs above the threshold (yellow line) to the 3 CpG pyrosequencing method on validation data, 18 males and 15 females were identified as contaminated. b Principal component plot of EPIC DNA methylation data on all non-contaminated samples with two male samples that had been called contaminated by pyrosequencing showed that contaminated male samples had been correctly identified. c Using the 10 CpG method from EPIC data, only the 2 male samples known to be contaminated had more than 5 CpGs above the threshold (red line)