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Methods for detecting methylation by SNP interaction in GAW20 simulation.

ABSTRACT: 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.

SUBMITTER: Daw EW

PROVIDER: S-EPMC6156982 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Methods for detecting methylation by SNP interaction in GAW20 simulation.

Daw E Warwick EW Hicks James J Lenzini Petra P Lin Shiow J SJ Wang Judy J Williams Christine C An Ping P Province Michael A MA Kraja Aldi T AT

BMC proceedings 20180917 Suppl 9

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 te ...[more]

PMID: 30263046

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