Methods for detecting methylation by SNP interaction in GAW20 simulation

To examine whether single-nucleotide polymorphism (SNP) by methylation interactions can be detected, we analyzed GAW20 simulated triglycerides at visits 3 and 4 against baseline (visits 1 and 2) under 4 general linear models and 2 tree-based models in 200 replications of a sample of 680 individuals....

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Autores principales: Daw, E. Warwick, Hicks, James, Lenzini, Petra, Lin, Shiow J., Wang, Judy, Williams, Christine, An, Ping, Province, Michael A., Kraja, Aldi T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Proceedings
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156982/
https://www.ncbi.nlm.nih.gov/pubmed/30263046
http://dx.doi.org/10.1186/s12919-018-0140-y
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author Daw, E. Warwick
Hicks, James
Lenzini, Petra
Lin, Shiow J.
Wang, Judy
Williams, Christine
An, Ping
Province, Michael A.
Kraja, Aldi T.
author_facet Daw, E. Warwick
Hicks, James
Lenzini, Petra
Lin, Shiow J.
Wang, Judy
Williams, Christine
An, Ping
Province, Michael A.
Kraja, Aldi T.
author_sort Daw, E. Warwick
collection PubMed
description To examine whether single-nucleotide polymorphism (SNP) by methylation interactions can be detected, we analyzed GAW20 simulated triglycerides at visits 3 and 4 against baseline (visits 1 and 2) under 4 general linear models and 2 tree-based models in 200 replications of a sample of 680 individuals. Effects for SNPs, methylation cytosine-phosphate-guanine (CpG) effects, and interactions for SNP/CpG pairs were included. Causative SNPs/CpG pairs distributed on autosomal chromosomes 1 to 20 were tested to examine sensitivity. We also tested noncausative SNP/CpG pairs on chromosomes 21 and 22 to estimate the empirical null. We found reasonable power to detect the main causative loci, with the exact power depending on sample size and strength of effects at the SNP and CpG sites.
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spelling pubmed-61569822018-09-27 Methods for detecting methylation by SNP interaction in GAW20 simulation Daw, E. Warwick Hicks, James Lenzini, Petra Lin, Shiow J. Wang, Judy Williams, Christine An, Ping Province, Michael A. Kraja, Aldi T. BMC Proc Proceedings To examine whether single-nucleotide polymorphism (SNP) by methylation interactions can be detected, we analyzed GAW20 simulated triglycerides at visits 3 and 4 against baseline (visits 1 and 2) under 4 general linear models and 2 tree-based models in 200 replications of a sample of 680 individuals. Effects for SNPs, methylation cytosine-phosphate-guanine (CpG) effects, and interactions for SNP/CpG pairs were included. Causative SNPs/CpG pairs distributed on autosomal chromosomes 1 to 20 were tested to examine sensitivity. We also tested noncausative SNP/CpG pairs on chromosomes 21 and 22 to estimate the empirical null. We found reasonable power to detect the main causative loci, with the exact power depending on sample size and strength of effects at the SNP and CpG sites. BioMed Central 2018-09-17 /pmc/articles/PMC6156982/ /pubmed/30263046 http://dx.doi.org/10.1186/s12919-018-0140-y Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Proceedings
Daw, E. Warwick
Hicks, James
Lenzini, Petra
Lin, Shiow J.
Wang, Judy
Williams, Christine
An, Ping
Province, Michael A.
Kraja, Aldi T.
Methods for detecting methylation by SNP interaction in GAW20 simulation
title Methods for detecting methylation by SNP interaction in GAW20 simulation
title_full Methods for detecting methylation by SNP interaction in GAW20 simulation
title_fullStr Methods for detecting methylation by SNP interaction in GAW20 simulation
title_full_unstemmed Methods for detecting methylation by SNP interaction in GAW20 simulation
title_short Methods for detecting methylation by SNP interaction in GAW20 simulation
title_sort methods for detecting methylation by snp interaction in gaw20 simulation
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156982/
https://www.ncbi.nlm.nih.gov/pubmed/30263046
http://dx.doi.org/10.1186/s12919-018-0140-y
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