Browsing by Subject "DNA methylation"

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    Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs
    (2017) Jones, Meaghan J
    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.
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    Open Access
    Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs
    (BioMed Central, 2017-07-25) Morin, Alexander M; Gatev, Evan; McEwen, Lisa M; MacIsaac, Julia L; Lin, David T S; Koen, Nastassja; Czamara, Darina; Räikkönen, Katri; Zar, Heather J; Koenen, Karestan; Stein, Dan J; Kobor, Michael S; Jones, Meaghan J
    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.
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    The role of mitochondria in autism: an analysis of mitochondrial dysfunction in ASD
    (2022) Van Der Colff, Rachelle; O'Ryan, Colleen
    Autism is a neurodevelopmental disorder characterised by challenges in socio-communication, restricted and repetitive behaviours and interests. Despite the 1 in 59 prevalence of ASD (Autism Spectrum Disorder), it is severely understudied in minority populations, such as the Sub-Saharan population. This is mainly because of a lack of genetic biobanks, meaning African researchers cannot compete with the large-scale studies of the Northern Hemisphere. The researchers involved in this project have previously set up a unique cohort of age-matched South African children with and without ASD. As epigenetics is becoming increasingly more popular in studying neuro-disorders, this research team has investigated the differential methylation (DM) patterns associated with ASD using a 450K array, and found several DM genes associated with mitochondrial metabolism. Hence the investigation into (and the title of this thesis) the association of mitochondrial dysfunction to ASD. This thesis aims to validate the differential methylation of a subset of these genes, to investigate STOML2 expression levels in ASD as a gene critical to mitochondrial fusion. Using different qPCR techniques, the relative mitochondrial copy number between ASD and neurotypical children was also analysed, looking at both copy number variation, and copy number deletion. This research successfully validated the DM of selected genes using two methods of validation, and identified both PCCB and PCDHA12 as significantly hypomethylated in children with ASD. A clear increase in mitochondrial copy number was also observed between ASD and neurotypical children. While mitochondrial deletions were not observed, this was to be expected because none of the ASD children in the cohort has any diagnosis of a severe mitochondrial disease (which would be clear phenotype of mitochondrial deletions). In conclusion, this thesis reinforces the role of mitochondria and its dysfunction in ASD.