Fig. 1

Evaluating PlaNET’s performance and characterizing ethnicity-predictive HM450K sites. We developed PlaNET (Placental elastic net ethnicity classifier), using placental HM450K data and evaluated its classification performance using leave-one-dataset-out cross validation. a Each sample’s ethnicity classification from PlaNET is shown with respect to their self-reported ethnicity. Samples were called ‘ambiguous’ if their predicted probability fell below a ‘confidence’ threshold of 75%. b PlaNET utilizes a subset of ethnicity-predictive sites from the HM450K. To investigate whether genetic signal is present in the measurement for these sites, we cross-referenced ethnicity-predictive sites to an existing placental mQTL database [42] and determined whether any sites had SNPs present in either the probe body, CpG site of interrogation, or single base extension sites, based on dbSNP137