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Published on: May 6, 2022
Paediatric DNA methylation profile scores: a systematic review and open-source atlas
Isabel K Schuurmans1, Serena Defina1, A P C Hermans1
1Department of Child and Adolescent Psychiatry and Psychology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
Insights
Methylation profile scores (MPSs) are increasingly used in early life research to understand exposures and health. This review highlights heterogeneity in studies and introduces DEMETRA, an atlas to guide selection of appropriate early-life MPSs.
Area of Science:
- Epigenetics and Developmental Biology
- Computational Biology and Bioinformatics
Background:
- Methylation profile scores (MPSs) aggregate DNA methylation (DNAm) data into a single metric.
- While widely used in adults, MPS application in early life (<18 years) is growing rapidly.
- Early-life DNAm offers insights into developmental exposures and disease vulnerability.
Purpose of the Study:
- To systematically review existing early-life MPS studies.
- To identify common limitations and sources of heterogeneity in early-life MPS research.
- To introduce DEMETRA, a resource for selecting appropriate early-life MPSs.
Main Methods:
- Systematic literature review of 119 early-life MPS studies.
- Analysis of 828 distinct MPSs across various exposures and traits.
- Development of DEMETRA, a searchable atlas of early-life MPSs.
Main Results:
- Significant heterogeneity observed in study design and reporting across the reviewed studies.
- Frequent use of MPSs trained on mismatched age groups, tissues, platforms, and ancestries.
- Potential for suboptimal MPS performance due to mismatched training data.
Conclusions:
- Early-life MPS research exhibits considerable heterogeneity and methodological inconsistencies.
- The DEMETRA atlas provides a valuable tool for researchers to identify and select suitable early-life MPSs.
- Standardizing MPS application in early life is crucial for reliable results and advancing developmental epigenetics research.
Abstract:
Methylation profile scores (MPSs) have emerged as a useful tool to index exposures, biological states, or disease-related patterns, by aggregating information across many DNA methylation (DNAm) sites into a single score per individual. Although most MPSs to date have been trained and validated in adults, their use in early life (<18 years) is rapidly gaining momentum, as more cohorts profile DNAm during development, offering a window on exposures and vulnerability before disease onset. Here we systematically review early-life MPS studies (n = 119), covering 828 MPSs that span a wide range of exposures and traits. Overall, studies show substantial heterogeneity in design and reporting. Also, studies frequently apply MPSs trained in data from mismatched age groups, tissues, array or platforms, and ancestries, which may influence MPS performance. To address these limitations, we introduce DEMETRA (indepthlab-demetra.share.connect.posit.cloud), a searchable atlas of early-life MPSs to help users identify and select scores best suited to their study.
