MMASS: an optimized array-based method for assessing CpG island methylation.
We describe an optimized microarray method for identifying genome-wide CpG island methylation called microarray-based methylation assessment of single samples (MMASS) which directly compares methylated to unmethylated sequences within a single sample. To improve previous methods we used bioinformatic analysis to predict an optimized combination of methylation-sensitive enzymes that had the highest utility for CpG-island probes and different methods to produce unmethylated representations of test DNA for more sensitive detection of differential methylation by hybridization. Subtraction or methylation-dependent digestion with McrBC was used with optimized (MMASS-v2) or previously described (MMASS-v1, MMASS-sub) methylation-sensitive enzyme combinations and compared with a published McrBC method. Comparison was performed using DNA from the cell line HCT116. We show that the distribution of methylation microarray data is inherently skewed and requires exogenous spiked controls for normalization and that analysis of digestion of methylated and unmethylated control sequences together with linear fit models of replicate data showed superior statistical power for the MMASS-v2 method. Comparison with previous methylation data for HCT116 and validation of CpG islands from PXMP4, SFRP2, DCC, RARB and TSEN2 confirmed the accuracy of MMASS-v2 results. The MMASS-v2 method offers improved sensitivity and statistical power for high-throughput microarray identification of differential methylation.
Ibrahim
Ashraf E K
AE
Department of Pathology, Division of Molecular Histopathology, Addenbrooke's Hospital Hills Road, Cambridge CB2 2XZ, UK. aeki2@cam.ac.uk
Thorne
Natalie P
NP
Baird
Katie
K
Barbosa-Morais
Nuno L
NL
Tavaré
Simon
S
Collins
V Peter
VP
Wyllie
Andrew H
AH
Arends
Mark J
MJ
Brenton
James D
JD
D045744:Cell Line, Tumor; D019295:Computational Biology; D018899:CpG Islands; D019175:DNA Methylation; D015342:DNA Probes / Q000737:chemistry; D004262:DNA Restriction Enzymes; D052138:Genes, Neoplasm; D023281:Genomics / Q000379:methods; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA
D015342:DNA Probes; D004262:DNA Restriction Enzymes; C120301:McrBC endonuclease