Epigenome-wide cross-tissue predictive modeling and comparison of cord blood and placental methylation in a birth cohort.
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ABSTRACT: Aim
We compared predictive modeling approaches to estimate placental methylation using cord blood methylation.Materials & methods
We performed locus-specific methylation prediction using both linear regression and support vector machine models with 174 matched pairs of 450k arrays.Results
At most CpG sites, both approaches gave poor predictions in spite of a misleading improvement in array-wide correlation. CpG islands and gene promoters, but not enhancers, were the genomic contexts where the correlation between measured and predicted placental methylation levels achieved higher values. We provide a list of 714 sites where both models achieved an R2 ≥0.75.Conclusion
The present study indicates the need for caution in interpreting cross-tissue predictions. Few methylation sites can be predicted between cord blood and placenta.
SUBMITTER: De Carli MM
PROVIDER: S-EPMC5331917 | biostudies-literature | 2017 Mar
REPOSITORIES: biostudies-literature
Publications
Epigenome-wide cross-tissue predictive modeling and comparison of cord blood and placental methylation in a birth cohort.
De Carli Margherita M MM Baccarelli Andrea A AA Trevisi Letizia L Pantic Ivan I Brennan Kasey Jm KJ Hacker Michele R MR Loudon Holly H Brunst Kelly J KJ Wright Robert O RO Wright Rosalind J RJ Just Allan C AC
Epigenomics 20170217 3
<h4>Aim</h4>We compared predictive modeling approaches to estimate placental methylation using cord blood methylation.<h4>Materials & methods</h4>We performed locus-specific methylation prediction using both linear regression and support vector machine models with 174 matched pairs of 450k arrays.<h4>Results</h4>At most CpG sites, both approaches gave poor predictions in spite of a misleading improvement in array-wide correlation. CpG islands and gene promoters, but not enhancers, were the genom ...[more]
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