Comparison of novel and existing methods for detecting differentially methylated regions

• Published in: BMC genetics Vol. 19; no. Suppl 1; p. 84
• Main Authors: Lent, Samantha, Xu, Hanfei, Wang, Lan, Wang, Zhe, Sarnowski, Chloé, Hivert, Marie-France, Dupuis, Josée
• Format: Journal Article
• Language: English
• Published: London BioMed Central 17.09.2018; BioMed Central Ltd; BMC
• Subjects: Animal Genetics and Genomics; Bioinformatics; Biomedical and Life Sciences; Carnitine O-Palmitoyltransferase - genetics; Chromosome 11; Chromosomes; Comparative analysis; CpG Islands; Deoxyribonucleic acid; Differentially methylated regions; Disease susceptibility; DNA; DNA Methylation; DNA probes; Epigenetic inheritance; Epigenetics; Epigenomics - methods; ETS Translocation Variant 6 Protein; Fenofibrate; Fenofibrate - therapeutic use; Genes; Genetic aspects; Genetics and Population Dynamics; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Humans; Hypertriglyceridemia - drug therapy; Hypertriglyceridemia - genetics; Hypoglycemic Agents - therapeutic use; Life Sciences; Lipids; Methods; Methylation; Microbial Genetics and Genomics; phenotype; Phenotypes; Physiological aspects; Plant Genetics and Genomics; Proto-Oncogene Proteins c-ets - genetics; Repressor Proteins - genetics; statistics; Studies; triacylglycerols; Triglycerides; Triglycerides - blood; United States; Epigenetics; DNA methylation; Differentially methylated regions
• ISSN: 1471-2156; 1471-2156
• DOI: 10.1186/s12863-018-0637-4

Background Single-probe analyses in epigenome-wide association studies (EWAS) have identified associations between DNA methylation and many phenotypes, but do not take into account information from neighboring probes. Methods to detect differentially methylated regions (DMRs) (clusters of neighboring probes associated with a phenotype) may provide more power to detect associations between DNA methylation and diseases or phenotypes of interest. Results We proposed a novel approach, GlobalP, and perform comparisons with 3 methods—DMRcate, Bumphunter, and comb-p—to identify DMRs associated with log triglycerides (TGs) in real GAW20 data before and after fenofibrate treatment. We applied these methods to the summary statistics from an EWAS performed on the methylation data. Comb-p, DMRcate, and GlobalP detected very similar DMRs near the gene CPT1A on chromosome 11 in both the pre- and posttreatment data. In addition, GlobalP detected 2 DMRs before fenofibrate treatment in the genes ETV6 and ABCG1 . Bumphunter identified several DMRs on chromosomes 1 and 20, which did not overlap with DMRs detected by other methods. Conclusions Our novel method detected the same DMR identified by two existing methods and detected two additional DMRs not identified by any of the existing methods we compared.