title: Evaluation of Methyl-Binding Domain Based Enrichment Approaches Revisited.
abstract: Methyl-binding domain (MBD) enrichment followed by deep sequencing (MBD-seq), is a robust and cost efficient approach for methylome-wide association studies (MWAS). MBD-seq has been demonstrated to be capable of identifying differentially methylated regions, detecting previously reported robust associations and producing findings that replicate with other technologies such as targeted pyrosequencing of bisulfite converted DNA. There are several kits commercially available that can be used for MBD enrichment. Our previous work has involved MethylMiner (Life Technologies, Foster City, CA, USA) that we chose after careful investigation of its properties. However, in a recent evaluation of five commercially available MBD-enrichment kits the performance of the MethylMiner was deemed poor. Given our positive experience with MethylMiner, we were surprised by this report. In an attempt to reproduce these findings we here have performed a direct comparison of MethylMiner with MethylCap (Diagenode Inc, Denville, NJ, USA), the best performing kit in that study. We find that both MethylMiner and MethylCap are two well performing MBD-enrichment kits. However, MethylMiner shows somewhat better enrichment efficiency and lower levels of background "noise". In addition, for the purpose of MWAS where we want to investigate the majority of CpGs, we find MethylMiner to be superior as it allows tailoring the enrichment to the regions where most CpGs are located. Using targeted bisulfite sequencing we confirmed that sites where methylation was detected by either MethylMiner or by MethylCap indeed were methylated.
authors.affiliation: Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, United States of America.
authors.forename: Karolina A
authors.initials: KA
authors.lastname: Aberg
authors.affiliation: Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, United States of America.
authors.forename: Linying
authors.initials: L
authors.lastname: Xie
authors.affiliation: Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, United States of America.
authors.forename: Robin F
authors.initials: RF
authors.lastname: Chan
authors.affiliation: Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, United States of America.
authors.forename: Min
authors.initials: M
authors.lastname: Zhao
authors.affiliation: Center for Integrative and Translational Genomics and Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, United States of America.
authors.forename: Ashutosh K
authors.initials: AK
authors.lastname: Pandey
authors.affiliation: Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, United States of America.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Kumar
authors.affiliation: Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, United States of America.
authors.forename: Shaunna L
authors.initials: SL
authors.lastname: Clark
authors.affiliation: Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, United States of America.
authors.forename: Edwin J C G
authors.initials: EJ
authors.lastname: van den Oord
mesh_terms: D000818:Animals; D018899:CpG Islands; D004247:DNA / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D019175:DNA Methylation; D016678:Genome; D008297:Male; D051379:Mice; D008811:Mice, Inbred DBA; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA