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Reference-free deconvolution of DNA methylation data and mediation by cell composition effects.
E Andres Houseman1, Molly L Kile2, David C Christiani3
1School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA. andres.houseman@oregonstate.edu.
BMC Bioinformatics
|July 1, 2016
Summary
We developed a novel reference-free deconvolution method for DNA methylation data. This approach identifies cell types and proportions in heterogeneous tissues, aiding biological interpretation without prior cell type information.
Area of Science:
- Genomics
- Computational Biology
- Epigenetics
Background:
- Supervised methods for DNA methylation deconvolution lack interpretability of cell types.
- Reference-free deconvolution is gaining interest for analyzing complex biological samples.
Purpose of the Study:
- To develop a simple, reference-free deconvolution method for DNA methylation data.
- To enable interpretation of underlying cell types and their proportions.
- To provide a method for evaluating the biological relevance of estimated methylomes.
Main Methods:
- Proposed a novel algorithm for reference-free deconvolution of DNA methylation data.
- Developed a method to estimate the number of constituent cell types.
- Created a metric to assess the biological specificity of estimated methylomes.
Main Results:
- Successfully applied the method to 23 Infinium datasets from 13 studies.
- Demonstrated accurate estimation of cell type numbers and proportions.
- Showed that estimated methylomes reflect the underlying biology of constituent cell types.
- Observed anticipated associations between cell proportions and phenotypic data.
Conclusions:
- The methodology allows explicit quantification of cell composition effects on DNA methylation-phenotype associations.
- Provides a foundation for studying DNA methylation in heterogeneous tissues without reference data.
- Offers a novel approach for understanding cell-type-specific contributions in epigenetics.
