Nimblegen Systems Adds Dna Methlyation Arrays And Services To Growing Product Portfolio (5/16/2007)

NimbleGen Systems, Inc. announced today the addition of DNA methylation analysis microarrays and services to its growing suite of genomic and epigenetic analysis tools. In addition to microarray designs allowing researchers to survey whole genomes, promoter regions, CpG islands, and ENCODE-defined regions, researchers can customize the content of their arrays based on individual study goals.

NimbleGen DNA methylation analysis arrays allow researchers to rapidly identify methylated regions in a high-throughput manner. These arrays can be used to correlate promoter and genic methylation with gene expression and/or phenotype and detect differential DNA methylation between normal tissues and tumor samples as potential diagnostic and prognostic markers.

Whole-genome DNA methylation arrays are available for human, mouse, rat, dog, and chicken genomes, tiling at an average probe spacing of 100bp to provide an unbiased approach to DNA methylation analysis. These arrays provide a distinct advantage, and differ from competitor products, by surveying not only regions surrounding known genes but also intergenic regions, allowing distal regulatory elements to be surveyed and providing the maximum opportunity to discover relevant biomarkers.

For studies focusing on promoter regions, one- and two-array sets are available for surveying promoter regions of all known genes in human, mouse, rat and Arabidopsis. In addition, NimbleGen’s CpG-Island Plus Promoter array design is the only one on the market that allows researchers to examine both CpG islands and RefSeq promoters with a single array. The human CpG-Island Plus Promoter design covers more than 28,000 CpG islands and 1kb of promoters from more than 25,000 RefSeq genes, providing superior coverage. A similar design is available for mouse as well.

Beta testing sites for NimbleGen’s DNA methylation analysis arrays were selected from premier cancer research centers, including the University of California-Davis; Radboud University, The Netherlands; and the City of Hope’s Beckman Research Institute, Calif.

"We’ve been very impressed with the comprehensiveness of the data we’ve obtained using a methylC antibody and NimbleGen genomic tiling arrays to analyze methylated DNA of human cancer cells," said Dr. Peggy Farnham, professor of pharmacology and associate director of genomics at the University of California-Davis. "This unbiased approach allows us to analyze any region of the genome, not just the small percentage that contains a specific restriction enzyme recognition site."

NimbleGen’s DNA methylation arrays are designed to detect methylated DNA fragments enriched by affinity-based methods, such as methylated DNA immunoprecipitation (MeDIP) or the MBD protein method. These arrays can detect as little as two to three 5-methyl cytosines in a 500bp genomic region, a task that is a challenge for other platforms to match. Dr. Henk Stunnenberg, head of the Department of Molecular Biology at Radboud University, The Netherlands, was enthused with NimbleGen’s unbiased, genome-wide approach to DNA methylation analysis. "Comparing the methylation profiles of healthy and diseased cells such as manifested in cancer cells, provides a wealth of information that will be instrumental in deciphering the molecular mechanisms pertaining to DNA methylation and its translation into a biological effect," he said. "Such analyses are likely to provide highly valuable novel diagnostic and prognostic biomarkers that enable tailoring of therapeutic treatment."

Dr. Gerd P. Pfeifer, co-leader of the Cancer Biology Program and chair and professor of Research Biology at the Beckman Research Institute, said, "We used the NimbleGen tiling arrays for DNA methylation studies with the methylated-CpG island recovery assay (MIRA). The data proved to be highly reproducible, and I think the quality of these arrays is superb. We were able to derive DNA methylation maps along chromosomal sequences with a high level of detail and accuracy."

Note: This story has been adapted from a news release issued by NimbleGen Systems Inc.

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