title: Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms.
abstract: In this study, we verified the accuracy of two array methods--methylated DNA immunoprecipitation coupled with CpG island microarrays (MeDIP-CGI-arrays) and sodium bisulfite conversion based microarrays (BC-arrays)--in predicting regional methylation levels as measured by pyrosequencing of bisulfite converted DNA (BC-pyrosequencing). To test the accuracy of these methods we used the Agilent Human CpG island and the Illumina HumanMethylation27 microarrays respectively, and compared microarray outputs to the data from targeted BC-pyrosequencing assays from several genomic regions of corresponding samples. We observed relatively high correlation with BC-pyrosequencing data for both array platforms, R = 0.87 for BC-Array and R = 0.79 for MeDIP-CGI array. However, MeDIP-CGI array were less reliable in predicting intermediate levels of DNA methylation. Several bioinformatics strategies, to ameliorate the performance of the MeDIP-CGI-Arrays did not improve the correlation with BC-pyrosequencing data. The high scalability, low cost and simpler analysis of BC-arrays, together with the recent extended coverage may make them a more versatile methylation analysis tool.
authors.affiliation: Program in Biological Sciences, University of Toronto, Ontario, Canada.
authors.forename: Rageen
authors.initials: R
authors.lastname: Rajendram
authors.forename: Jose Carlos
authors.initials: JC
authors.lastname: Ferreira
authors.forename: Daria
authors.initials: D
authors.lastname: Grafodatskaya
authors.forename: Sanaa
authors.initials: S
authors.lastname: Choufani
authors.forename: Theodore
authors.initials: T
authors.lastname: Chiang
authors.forename: Shuye
authors.initials: S
authors.lastname: Pu
authors.forename: Darci T
authors.initials: DT
authors.lastname: Butcher
authors.forename: Shoshana J
authors.initials: SJ
authors.lastname: Wodak
authors.forename: Rosanna
authors.initials: R
authors.lastname: Weksberg
mesh_terms: D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA; D013431:Sulfates
chemical_list: D013431:Sulfates; C012036:sodium sulfate