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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Detalles Bibliográficos
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
Descripción
Sumario: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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