High-throughput DNA methylation profiling using universal bead arrays.

By M. Bibikova, Zhenwu Lin, Lixin Zhou, E. Chudin, Eliza Wickham Garcia, Bonnie Wu, Dennis Doucet, Neal J. Thomas, Yunhua Wang, E. Vollmer and 7 more. Genome Research, 2006

689 citations recorded by the source corpus.

We have developed a high-throughput method for analyzing the methylation status of hundreds of preselected genes simultaneously and have applied it to the discovery of methylation signatures that distinguish normal from cancer tissue samples. Through an adaptation of the GoldenGate genotyping assay implemented on a BeadArray platform, the methylation state of 1536 specific CpG sites in 371 genes (one to nine CpG sites per gene) was measured in a single reaction by multiplexed genotyping of 200 ng of bisulfite-treated genomic DNA. The assay was used to obtain a quantitative measure of the methylation level at each CpG site. After validating the assay in cell lines and normal tissues, we analyzed a panel of lung cancer biopsy samples (N = 22) and identified a panel of methylation markers that distinguished lung adenocarcinomas from normal lung tissues with high specificity. These markers were validated in a second sample set (N = 24). These results demonstrate the effectiveness of the method for reliably profiling many CpG sites in parallel for the discovery of informative methylation markers. The technology should prove useful for DNA methylation analyses in large populations, with potential application to the classification and diagnosis of a broad range of cancers and other diseases.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7d996ae76798cc9e39dfb7d024f4b08e4b17b3f5

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In Molecular Biology

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Citations in the corpus

• Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context (2009, methodology): “Bead arrays have a similar sensitivity as quantitative methylation-specific PCR and were run at the UCSF Institute for Human Genetics, Genomics Core Facility according to the manufacturer’s protocol and as described by Bibikova et al [43].”
• Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. (2006, methodology): “For example, the methylation status of 1534 CpG sites was assessed using a mixture of ∼6000 primers (Bibikova et al. 2005).”
• Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. (2010, methodology): “…survey the DNA methylation of up to 1536 CpG sites—a total of 1505 CpGs spanning 807 unique gene loci are interrogated in the OMA-002 probe set (Bibikova et al., 2006), and 1498 CpGs spanning the same number of unique gene regions are investigated in the OMA-003 probe set (The Cancer Genome…”
• Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis (2010, methodology): “Following the notation used by Illumina methylation assay [12], Beta-value for an i interrogated CpG site is defined as:”
• SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions (2018, background): “DNA methylation readouts from these arrays are usually expressed in β values (10), defined as β = Max(M, 0)/(Max(M, 0) + Max(U, 0) + α), in which M represents the hybridization signal from a methylated version and U represents the hybridization signal from an unmethylated version of a cytosine nucle”
• Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. (2010, methodology): “Specifically, we performed DNA methylation profiling using universal bead arrays (Bibikova et al. 2006)with 60 samples corresponding toDNAextracted fromwhite blood cells (WBCs) of 30MZ twins discordant for SLE, RA, and DM (five twin pairs of each disease), and 30 unrelated normal controls matching b”
• Increased methylation variation in epigenetic domains across cancer types (2011, neutral): “The increased comprehensiveness of sequencing over CHARM and other published array-based analyses allowed us to detect more small DMRs than previously reported, 5,810 hypermethylated and 4,315 hypomethylated small DMRs (Supplementary Table 7).”
• Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. (2006, background): “Recent advances in sequencing technology have made it possible to assay over 1,000 preselected CG sites in hundreds of genes (Bibikova et al., 2006).”
• Principles and challenges of genome-wide DNA methylation analysis (2010, methodology): “Multiplexed methylation-specific primer extension of bisulphite-converted DNA at up to 1,536 different CpG sites is performed using primers that are specific for methylated and unmethylated sequences at each sit”