Morin, Alexander M.Gatev, EvanMcEwen, Lisa M.MacIsaac, Julia L.Lin, David T. S.Koen, NastassjaCzamara, DarinaRäikkönen, KatriZar, Heather J.Koenen, KarestanStein, Dan J.Kobor, Michael S.Jones, Meaghan J.2017-11-212017Morin, A. M., E. Gatev, L. M. McEwen, J. L. MacIsaac, D. T. S. Lin, N. Koen, D. Czamara, et al. 2017. “Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs.” Clinical Epigenetics 9 (1): 75. doi:10.1186/s13148-017-0370-2. http://dx.doi.org/10.1186/s13148-017-0370-2.http://nrs.harvard.edu/urn-3:HUL.InstRepos:34375329Background: Cord blood is a commonly used tissue in environmental, genetic, and epigenetic population studies due to its ready availability and potential to inform on a sensitive period of human development. However, the introduction of maternal blood during labor or cross-contamination during sample collection may complicate downstream analyses. After discovering maternal contamination of cord blood in a cohort study of 150 neonates using Illumina 450K DNA methylation (DNAm) data, we used a combination of linear regression and random forest machine learning to create a DNAm-based screening method. We identified a panel of DNAm sites that could discriminate between contaminated and non-contaminated samples, then designed pyrosequencing assays to pre-screen DNA prior to being assayed on an array. Results: Maternal contamination of cord blood was initially identified by unusual X chromosome DNA methylation patterns in 17 males. We utilized our DNAm panel to detect contaminated male samples and a proportional amount of female samples in the same cohort. We validated our DNAm screening method on an additional 189 sample cohort using both pyrosequencing and DNAm arrays, as well as 9 publically available cord blood 450K data sets. The rate of contamination varied from 0 to 10% within these studies, likely related to collection specific methods. Conclusions: Maternal blood can contaminate cord blood during sample collection at appreciable levels across multiple studies. We have identified a panel of markers that can be used to identify this contamination, either post hoc after DNAm arrays have been completed, or in advance using a targeted technique like pyrosequencing. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0370-2) contains supplementary material, which is available to authorized users.en-USCord bloodContaminationDNA methylation450KGenotypingMaternal bloodBlood bankingJournal Article2017-11-2110.1186/s13148-017-0370-2