Biomarker Discovery: MethylScope® Technology
We are able to simultaneously study every human gene, and millions of other loci
Orion's patented MethylScope® technology, first published in Nature 2004, enables genome-wide DNA methylation profiling. MethylScope technology is a best in class DNA analysis tool compatible with microarray, bead array and all next generation DNA sequencing technologies. MethylScope technology allows Orion and its partners to simultaneously study the epigenetic state of every gene as well as millions of other loci within the genome. Orion's scientists leverage MethylScope technology in our strategic alliances to discover DNA methylation biomarkers important in epigenetic disorders like cancer, or in agronomic traits such as yield.
MethylScope technology was invented by Robert Martienssen, Professor at Cold Spring Harbor Laboratory, a scientific founder of Orion, and winner of Science's Breakthrough of the Year. Orion received an exclusive license to commercialize MethylScope technology from Cold Spring Harbor Laboratory in 2003. The seminal patent covering MethylScope technology issued on March 6, 2007.
Process
The MethylScope process involves quantifying at least one DNA sequence in a population of DNA fragments, where the population of DNA fragments has been enriched for methylated (or alternatively unmethylated) DNA sequences.
One way to practice MethylScope technology involves splitting DNA extracted from a specimen into two fractions. Methylated DNA fragments are removed from one fraction, and the remaining DNA - now enriched for unmethylated DNA fragments - is labeled with a first fluorescent dye (e.g., green). The other whole genome fraction is not treated and is then labeled with a second fluorescent dye (e.g., red). The dye-labeled fragments are then hybridized to a MethylScope array. The array is scanned and red:green ratios are determined for each spot, resulting in a high-resolution methylation profile of all of the genes in the sample.
The microarrays used for MethylScope analysis consist of > 1 million spots, each containing a unique 50 to 60 base DNA sequence that has been synthesized at high density onto a microarray. The DNA features on the MethylScope array have been designed by Orion's informatics team to comprehensively represent the human genome.
The above figure displays an image of a microarray hybridized with human DNA analyzed using MethylScope technology. Features that are green correspond to 1,000 base pair regions of human genes with the lowest methylation densities, while yellow features represent gene regions with moderate methylation, and red features have the highest methylation densities. With MethylScope technology, quantitative methylation profiling of all genes in the human genome is performed in one experiment on a single array.
Biomarker Discovery
Orion discovers biomarkers by comparing methylation profiles from panels of normal tissue samples with methylation profiles from panels of tumor samples and finding the markers that differentiate the two sample types. These biomarkers are incorporated into diagnostic tests now in develoment at Orion and are enhancing the value of Orion's patent portfolio. Similarly, biomarkers useful for therapy selection tests are discovered by comparing methylation profiles from responding and non-responding panels of tumors. Supporting our biomarker discovery efforts are the numerous clinical collaborations we have formed with academic investigators at institutions worldwide, including Johns Hopkins University, the University of Glasgow, and Mayo Clinical Laboratory Services.
MethylScope Publications
Lippman, et al. (2004) Nature 430: 471-6.
Lippman, et al. (2005) Nature Methods 2: 219-24.
Ordway, et al. (2006) Carcinogenesis 27: 2409-23.
Vaughn, et al. (2007) PLoS Biology 5: e174.
Ordway, et al. (2007) PLoS ONE 2: e1314.
Korshunova, et al. (2008) Genome Res 18: 19-29.
Irizarry, et al. (2008) Genome Res 18: 780-90.
Ladd-Acosta, et al. (2010) Curr Protoc Hum Genet 20(1): 1-19.