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. 2018 Sep 17;12(Suppl 9):37.
doi: 10.1186/s12919-018-0140-y. eCollection 2018.

Methods for detecting methylation by SNP interaction in GAW20 simulation

E Warwick Daw  1 , James Hicks  1 , Petra Lenzini  1 , Shiow J Lin  1 , Judy Wang  1 , Christine Williams  1 , Ping An  1 , Michael A Province  1 , Aldi T Kraja  1
Affiliations

Methods for detecting methylation by SNP interaction in GAW20 simulation

E Warwick Daw et al. BMC Proc. .

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.

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Conflict of interest statement

Not applicable.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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