ArticleNucleic acids research2006
MMASS: an optimized array-based method for assessing CpG island methylation.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 47 citations in OpenAlex.
- Laboratory methods to decipher epigenetic signatures: a comparative review.Cellular & molecular biology letters · 2021Review
- Influence of relative NK-DC abundance on placentation and its relation to epigenetic programming in the offspring.Cell death & disease · 2014Article
- DNA methylation analysis in human cancer.Methods in molecular biology (Clifton, N.J.) · 2013Article
- Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers.Cancer medicine · 2012Review
- Hypermethylation of the gene LARP2 for noninvasive prenatal diagnosis of β-thalassemia based on DNA methylation profile.Molecular biology reports · 2012Article
- Hypermethylation of IGSF4 gene for noninvasive prenatal diagnosis of thalassemia.Medical science monitor : international medical journal of experimental and clinical research · 2012Article
- Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer.European journal of human genetics : EJHG · 2011Article
- Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array.BMC genomics · 2011Article
- Profiling DNA methylomes from microarray to genome-scale sequencing.Technology in cancer research & treatment · 2010Review
- Experimental approaches to the study of epigenomic dysregulation in ageing.Experimental gerontology · 2010Review
- Principles and challenges of genomewide DNA methylation analysis.Nature reviews. Genetics · 2010Review
- Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation.Nucleic acids research · 2009Article
- DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status.Leukemia · 2008Article
- Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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