Zhou, Z., Lunetta, K. L., Smith, A. K., Wolf, E., Stone, A., Schichman, S., McGlinchey, R., Milberg, W., Miller, M. W., & Logue, M. (2019). Correction for multiple testing in candidate-gene methylation studies. Epigenomics, 11, Article 9. (Original work published 2026)
Aim: We compared the performance of multiple testing corrections for candidate gene methylation studies, namely Sidak (accurate Bonferroni), false-discovery rate and three adjustments that incorporate the correlation between CpGs: extreme tail theory (ETT), Gao et al. (GEA), and Li and Ji methods. Materials & methods: The experiment-wide type 1 error rate was examined in simulations based on Illumina EPIC and 450K data. Results: For high-correlation genes, Sidak and false-discovery rate corrections were conservative while the Li and Ji method was liberal. The GEA method tended to be conservative unless a threshold parameter was adjusted. The ETT yielded an appropriate type 1 error rate. Conclusion: For genes with substantial correlation across measured CpGs, GEA and ETT can appropriately correct for multiple testing in candidate gene methylation studies.
