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A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics

Epigenetic sex differences and their resulting implications for human health have been studied for about a decade. The objective of this paper is to use permutation-based inference and a new ranked-based test statistic to identify sex-based epigenetic differences in the human DNA methylome. In parti...

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Autores principales: Sommer, Alice J., Okonkwo, Jude, Monteiro, Jonathan, Bind, Marie-Abèle C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10491832/
https://www.ncbi.nlm.nih.gov/pubmed/37684282
http://dx.doi.org/10.1038/s41598-023-41360-6
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author Sommer, Alice J.
Okonkwo, Jude
Monteiro, Jonathan
Bind, Marie-Abèle C.
author_facet Sommer, Alice J.
Okonkwo, Jude
Monteiro, Jonathan
Bind, Marie-Abèle C.
author_sort Sommer, Alice J.
collection PubMed
description Epigenetic sex differences and their resulting implications for human health have been studied for about a decade. The objective of this paper is to use permutation-based inference and a new ranked-based test statistic to identify sex-based epigenetic differences in the human DNA methylome. In particular, we examine whether we could identify separations between the female and male distributions of DNA methylation across hundred of thousands CpG sites in two independent cohorts, the Swedish Adoption Twin study and the Lamarck study. Based on Fisherian p-values, we set a threshold for methylation differences “worth further scrutiny”. At this threshold, we were able to confirm previously-found CpG sites that stratify with respect to sex. These CpG sites with sex differences in DNA methylation should be further investigated for their possible contribution to various physiological and pathological functions in the human body. We followed-up our statistical analyses with a literature review in order to inform the proposed disease implications for the loci we uncovered.
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spelling pubmed-104918322023-09-10 A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics Sommer, Alice J. Okonkwo, Jude Monteiro, Jonathan Bind, Marie-Abèle C. Sci Rep Article Epigenetic sex differences and their resulting implications for human health have been studied for about a decade. The objective of this paper is to use permutation-based inference and a new ranked-based test statistic to identify sex-based epigenetic differences in the human DNA methylome. In particular, we examine whether we could identify separations between the female and male distributions of DNA methylation across hundred of thousands CpG sites in two independent cohorts, the Swedish Adoption Twin study and the Lamarck study. Based on Fisherian p-values, we set a threshold for methylation differences “worth further scrutiny”. At this threshold, we were able to confirm previously-found CpG sites that stratify with respect to sex. These CpG sites with sex differences in DNA methylation should be further investigated for their possible contribution to various physiological and pathological functions in the human body. We followed-up our statistical analyses with a literature review in order to inform the proposed disease implications for the loci we uncovered. Nature Publishing Group UK 2023-09-08 /pmc/articles/PMC10491832/ /pubmed/37684282 http://dx.doi.org/10.1038/s41598-023-41360-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This 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/) .
spellingShingle Article
Sommer, Alice J.
Okonkwo, Jude
Monteiro, Jonathan
Bind, Marie-Abèle C.
A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics
title A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics
title_full A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics
title_fullStr A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics
title_full_unstemmed A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics
title_short A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics
title_sort permutation-based approach using a rank-based statistic to identify sex differences in epigenetics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10491832/
https://www.ncbi.nlm.nih.gov/pubmed/37684282
http://dx.doi.org/10.1038/s41598-023-41360-6
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