An overview of DNA methylation-derived trait score methods and applications

Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites (“probes”) and complex traits or diseases. The results can be used to generate methylation profile scores (MP...

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Autores principales: Nabais, Marta F., Gadd, Danni A., Hannon, Eilis, Mill, Jonathan, McRae, Allan F., Wray, Naomi R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Review
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9936670/
https://www.ncbi.nlm.nih.gov/pubmed/36797751
http://dx.doi.org/10.1186/s13059-023-02855-7
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author Nabais, Marta F.
Gadd, Danni A.
Hannon, Eilis
Mill, Jonathan
McRae, Allan F.
Wray, Naomi R.
author_facet Nabais, Marta F.
Gadd, Danni A.
Hannon, Eilis
Mill, Jonathan
McRae, Allan F.
Wray, Naomi R.
author_sort Nabais, Marta F.
collection PubMed
description Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites (“probes”) and complex traits or diseases. The results can be used to generate methylation profile scores (MPS) to predict outcomes in independent data sets. Although there are many parallels between MPS and polygenic (risk) scores (PGS), there are key differences. Here, we review motivations, methods, and applications of DNA methylation-based trait prediction, with a focus on common diseases. We contrast MPS with PGS, highlighting where assumptions made in genetic modeling may not hold in epigenetic data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02855-7.
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spelling pubmed-99366702023-02-18 An overview of DNA methylation-derived trait score methods and applications Nabais, Marta F. Gadd, Danni A. Hannon, Eilis Mill, Jonathan McRae, Allan F. Wray, Naomi R. Genome Biol Review Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites (“probes”) and complex traits or diseases. The results can be used to generate methylation profile scores (MPS) to predict outcomes in independent data sets. Although there are many parallels between MPS and polygenic (risk) scores (PGS), there are key differences. Here, we review motivations, methods, and applications of DNA methylation-based trait prediction, with a focus on common diseases. We contrast MPS with PGS, highlighting where assumptions made in genetic modeling may not hold in epigenetic data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02855-7. BioMed Central 2023-02-16 /pmc/articles/PMC9936670/ /pubmed/36797751 http://dx.doi.org/10.1186/s13059-023-02855-7 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Review
Nabais, Marta F.
Gadd, Danni A.
Hannon, Eilis
Mill, Jonathan
McRae, Allan F.
Wray, Naomi R.
An overview of DNA methylation-derived trait score methods and applications
title An overview of DNA methylation-derived trait score methods and applications
title_full An overview of DNA methylation-derived trait score methods and applications
title_fullStr An overview of DNA methylation-derived trait score methods and applications
title_full_unstemmed An overview of DNA methylation-derived trait score methods and applications
title_short An overview of DNA methylation-derived trait score methods and applications
title_sort overview of dna methylation-derived trait score methods and applications
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9936670/
https://www.ncbi.nlm.nih.gov/pubmed/36797751
http://dx.doi.org/10.1186/s13059-023-02855-7
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