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

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dc.contributor.authorJones, Meaghan J
dc.date.accessioned2021-10-08T06:55:02Z
dc.date.available2021-10-08T06:55:02Z
dc.date.issued2017
dc.description.abstractAbstract Background 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.
dc.identifier.apacitationJones, M. J. (2017). Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs. <i>Clinical Epigenetics</i>, 9(1), 174 - 177. http://hdl.handle.net/11427/34400en_ZA
dc.identifier.chicagocitationJones, Meaghan J "Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs." <i>Clinical Epigenetics</i> 9, 1. (2017): 174 - 177. http://hdl.handle.net/11427/34400en_ZA
dc.identifier.citationJones, M.J. 2017. Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs. <i>Clinical Epigenetics.</i> 9(1):174 - 177. http://hdl.handle.net/11427/34400en_ZA
dc.identifier.issn1868-7075
dc.identifier.issn1868-7083
dc.identifier.ris TY - Journal Article AU - Jones, Meaghan J AB - Abstract Background 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. DA - 2017 DB - OpenUCT DP - University of Cape Town IS - 1 J1 - Clinical Epigenetics LK - https://open.uct.ac.za PY - 2017 SM - 1868-7075 SM - 1868-7083 T1 - Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs TI - Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs UR - http://hdl.handle.net/11427/34400 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/34400
dc.identifier.vancouvercitationJones MJ. Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs. Clinical Epigenetics. 2017;9(1):174 - 177. http://hdl.handle.net/11427/34400.en_ZA
dc.language.isoeng
dc.publisher.departmentDepartment of Psychiatry and Mental Health
dc.publisher.facultyFaculty of Health Sciences
dc.sourceClinical Epigenetics
dc.source.journalissue1
dc.source.journalvolume9
dc.source.pagination174 - 177
dc.source.urihttps://dx.doi.org/10.1186/s13148-017-0370-2
dc.subject.other450K
dc.subject.otherBlood banking
dc.subject.otherContamination
dc.subject.otherCord blood
dc.subject.otherDNA methylation
dc.subject.otherGenotyping
dc.subject.otherMaternal blood
dc.subject.otherCohort Studies
dc.subject.otherCpG Islands
dc.subject.otherDNA
dc.subject.otherDNA Contamination
dc.subject.otherDNA Methylation
dc.subject.otherEpigenesis, Genetic
dc.subject.otherFemale
dc.subject.otherFetal Blood
dc.subject.otherHumans
dc.subject.otherInfant, Newborn
dc.subject.otherLinear Models
dc.subject.otherMale
dc.subject.otherMothers
dc.subject.otherOligonucleotide Array Sequence Analysis
dc.subject.otherSequence Analysis, DNA
dc.subject.otherDNA
dc.titleMaternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs
dc.typeJournal Article
uct.type.publicationResearch
uct.type.resourceJournal Article
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