Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms.

TitleAssessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms.
Publication TypeJournal Article
Year of Publication2011
AuthorsRajendram, R., Ferreira J. Carlos, Grafodatskaya D., Choufani S., Chiang T., Pu S., Butcher D. T., Wodak S. J., and Weksberg R.
JournalEpigenetics
Volume6
Issue4
Pagination410-5
Date Published2011 Apr
ISSN1559-2308
KeywordsCpG Islands, DNA Methylation, Humans, Immunoprecipitation, Oligonucleotide Array Sequence Analysis, Sequence Analysis, DNA, Sulfates
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.

Alternate JournalEpigenetics
PubMed ID21343703