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Clin Epigenetics. 2017 Jul 25;9:75. doi: 10.1186/s13148-017-0370-2. eCollection 2017.

Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs.

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Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Department of Medical Genetics, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada.
Department of Psychiatry and Mental Health, South African Medical Research Council (SAMRC) Unit on Anxiety and Stress Disorders, University of Cape Town, Groote Schuur Hospital, J2, Anzio Road, Observatory, Cape Town, South Africa.
Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Kraepelinstraße 2-10, 80804 Munich, Germany.
Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014 Helsinki, Finland.
Department of Paediatrics, MRC Unit on Child and Adolescent Health, University of Cape Town, Room 513 ICH Building Red Cross Children's Hospital Klipfontein Road, Cape Town, South Africa.
Department of Epidemiology, Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Kresge Building, 505, Boston, MA 02115 USA.
Human Early Learning Partnership, University of British Columbia, 2208 East Mall, Vancouver, BC 02115 Canada.



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.


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.


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.


450K; Blood banking; Contamination; Cord blood; DNA methylation; Genotyping; Maternal blood

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