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Series GSE5326 Query DataSets for GSE5326
Status Public on Oct 31, 2006
Title MMASS: an optimised array-based method for assessing CpG island
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary 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 optimised 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 to 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 to 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.
Keywords: Methylation genomic hybridizations.
 
Overall design For each of the methods we obtained four microarray hybridisations, using replicate biological preparations in a balanced dye-swap design and compared the results to the published method of Nouzova et al. DNA from the colorectal cancer cell line HCT116 was used for all experiments as methylation patterns have been well characterized in this cell lin
 
Contributor(s) Ibrahim AE, Thorne NP, Morais NB, Arends MJ, Brenton JD
Citation(s) 17041235
Submission date Jul 17, 2006
Last update date Mar 16, 2012
Contact name Ashraf Ibrahim
E-mail(s) aeki2@cam.ac.uk
Phone 01223586942
Fax 01223 586670
Organization name Univeristy of Cambridge
Department Pathology
Lab Molecular Histopathology
Street address Hills Road
City Cambridge
ZIP/Postal code CB2 2QQ
Country United Kingdom
 
Platforms (1)
GPL2040 UHN Human CpG 12K Array (HCGI12K)
Samples (16)
GSM121581 MMASS: an optimised array-based method for assessing CpG island (MMASS_sub) array_1)
GSM121582 MMASS: an optimised array-based method for assessing CpG island (MMASS_sub) array_4
GSM121583 MMASS: an optimised array-based method for assessing CpG island (MMASS_sub) array_3
Relations
BioProject PRJNA96339

Download family Format
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