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Epigenomics to Upgrade Methylation Service As It Considers Broadening Access to Chips

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Epigenomics recently said it plans to add a new mouse-specific methylation array to its differential methylation hybridization research service in the second quarter, and is considering ways of making its flagship research tool, the human DMH array, more broadly available.
 
Epigenomics hopes the mouse DMH array will meet demand from its major pharmaceutical and biotech customers, spokesperson Achim Plum told BioArray News two weeks ago.
 
"When talking to our partners, we realized a high need for DMH arrays for animal models,” Plum said.
 
He said the mouse array will have similar coverage as the company’s human DMH array, but “special emphasis will be put on regions that are congenic with humans,” Plum said.
 
According to Plum, the majority of Epigenomics’ customers are “pharmas and biotechs, many of which belong to the top-10 companies in their category.” Plum added that in these partnerships, Epigenomics usually provides “not just the DMH service but … [also] experimental design, data analysis, and data interpretation.”
 
As for the human DMH array, which covers more than 50,000 human genomic fragments, Epigenomics currently offers it as a screening tool as part of its biomarker-discovery services. Plum said that the firm doesn’t plan to upgrade the array in the next few months, although it has “streamlined the sample processing workflow, increased throughput, and further improved raw data analysis and data quality control” over the past year.
 
 “The layout we offer to our customers now is already a second generation and still state of the art,” Plum said. “Certainly we will consider an upgrade as new data becomes available that provides a rational basis for improving the design.”
Plum said that Epigenomics is now considering ways to make it more available to researchers, including those in the academic life sciences community.
 
“Currently we only offer the DMH arrays as service to our partners. As we realize a high need for our DMH in the life science community, we do intend to offer these arrays more broadly in the future, but so far no decisions [have been made regarding] how and when we will do this," he said.
 
Plum declined to say which specific avenues Epigenomics was considering for broadening accessibility to the DMH array. “We are evaluating several options but it is too early to tell how and when we will offer it more broadly. In the mean time, interested parties can make use of our DMH service,” he said.
 
Plum also said that Epigenomics’ DMH service has been indirectly bolstered by research conducted by the Human Epigenome Consortium, which aims to identify, catalogue, and interpret genome-wide DNA methylation patterns of all human genes in all major tissues.
 
Epigenomics is a member of the HEC. Other members include the Wellcome Trust Sanger Institute and the French National Genotyping Center.
 
"We believe that looking at every single CpG in the genome will not help to extract relevant data,” Plum said. “Broad DNA methylation approaches like the Human Epigenome Project ... will help to better characterize which regions of the genome have the potential to carry functionally relevant DNA methylation information,” he said.
 

“Currently we only offer the DMH arrays as a service to our partners. As we realize a high need for our DMH in the life science community, we do intend to offer these arrays more broadly in the future.”

“Our DMH array is a first step towards targeting these regions as it includes the knowledge we gained in the HEP,” he added. “As research moves along, further improvements will be possible."
 
Prostate Cancer Prognostic
 
Plum said that Epigenomics is on track to release sometime next year an in vitro prostate cancer prognostic that is applied to formalin-fixed paraffin-embedded tumor tissue samples. Plum said that the company is considering launching the test first as a homebrew and then moving forward with a 510 (k) submission to the US Food and Drug Administration.
 
 “We just successfully transferred our prognostic prostate cancer marker PITX2 on the Affymetrix platform. The test is now in development under medical device standards,” Plum said. “As a fast track to the market, we are currently considering a launch in 2008 as a homebrew test through reference laboratories in the US.”
 
The company also said several months ago that it was considering submitting the test for US Food and Drug Administration clearance sometime next year (see BAN 12/13/2006).

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