AIMS: To compare the performance of four sequence-based and one microarray methods for DNA methylation profiling. METHODS: DNA from two cell lines were profiled by reduced representation bisulfite sequencing, methyl capture sequencing (SS-Meth Seq), NimbleGen SeqCapEpi CpGiant(Nimblegen MethSeq), methylated DNA immunoprecipitation (MeDIP) and the Human Methylation 450 Bead Chip (Meth450K). RESULTS & CONCLUSION: Despite differences in genome-wide coverage, high correlation and concordance were observed between different methods. Significant overlap of differentially methylated regions was identified between sequenced-based platforms. MeDIP provided the best coverage for the whole genome and gene body regions, while RRBS and Nimblegen MethSeq were superior for CpGs in CpG islands and promoters. Methylation analyses can be achieved by any of the five methods but understanding their differences may better address the research question being posed.
AIMS: To compare the performance of four sequence-based and one microarray methods for DNA methylation profiling. METHODS: DNA from two cell lines were profiled by reduced representation bisulfite sequencing, methyl capture sequencing (SS-Meth Seq), NimbleGen SeqCapEpi CpGiant(Nimblegen MethSeq), methylated DNA immunoprecipitation (MeDIP) and the Human Methylation 450 Bead Chip (Meth450K). RESULTS & CONCLUSION: Despite differences in genome-wide coverage, high correlation and concordance were observed between different methods. Significant overlap of differentially methylated regions was identified between sequenced-based platforms. MeDIP provided the best coverage for the whole genome and gene body regions, while RRBS and Nimblegen MethSeq were superior for CpGs in CpG islands and promoters. Methylation analyses can be achieved by any of the five methods but understanding their differences may better address the research question being posed.
Authors: Karolina A Aberg; Robin F Chan; Andrey A Shabalin; Min Zhao; Gustavo Turecki; Nicklas Heine Staunstrup; Anna Starnawska; Ole Mors; Lin Y Xie; Edwin Jcg van den Oord Journal: Epigenetics Date: 2017-11-06 Impact factor: 4.528
Authors: Rohit R Jadhav; Yao V Wang; Ya-Ting Hsu; Joseph Liu; Dawn Garcia; Zhao Lai; Tim H M Huang; Victor X Jin Journal: J Vis Exp Date: 2016-10-31 Impact factor: 1.355
Authors: Scott Gigante; Quentin Gouil; Alexis Lucattini; Andrew Keniry; Tamara Beck; Matthew Tinning; Lavinia Gordon; Chris Woodruff; Terence P Speed; Marnie E Blewitt; Matthew E Ritchie Journal: Nucleic Acids Res Date: 2019-05-07 Impact factor: 16.971
Authors: Stine T Bak; Nicklas H Staunstrup; Anna Starnawska; Tina F Daugaard; Jens R Nyengaard; Mette Nyegaard; Anders Børglum; Ole Mors; Karl-Anton Dorph-Petersen; Anders L Nielsen Journal: Mol Neurobiol Date: 2016-12-19 Impact factor: 5.590
Authors: Lin Han; Hua-Jun Wu; Haiying Zhu; Kun-Yong Kim; Sadie L Marjani; Markus Riester; Ghia Euskirchen; Xiaoyuan Zi; Jennifer Yang; Jasper Han; Michael Snyder; In-Hyun Park; Rafael Irizarry; Sherman M Weissman; Franziska Michor; Rong Fan; Xinghua Pan Journal: Nucleic Acids Res Date: 2017-06-02 Impact factor: 16.971