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

作者：Rajendram Rageen; Ferreira Jose C; Grafodatskaya Daria; Choufani Sanaa; Chiang Theodore; Pu Shuye; Butcher Darci T; Wodak Shoshana J; Wek**erg Rosanna^*

来源：Epigenetics, 2011, 6(4): 410-416.

DOI：10.4161/epi.6.4.14763

• DNA methylation
• CpG island
• pyrosequencing
• MeDIP
• batman algorithm

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.

• 出版日期2011-4