Journal
EPIGENETICS
Volume 6, Issue 4, Pages 410-416Publisher
TAYLOR & FRANCIS INC
DOI: 10.4161/epi.6.4.14763
Keywords
DNA methylation; CpG island; pyrosequencing; MeDIP; batman algorithm
Funding
- Canadian Institutes of Health Research [MOP86758]
- POPH (Operational Program for Human Potential) [SFRH/BD/28642/2006]
- MCTES (Ministry of Science, Technology and Higher Education)
- McGill University, Montreal
- Agilent Technologies
- Fundação para a Ciência e a Tecnologia [SFRH/BD/28642/2006] Funding Source: FCT
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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 Human Methylation27 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.
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