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Kreatech Inks Pact with Hungarian University to Develop FFPE Sample-Handling Methods for Array-CGH


By Justin Petrone

Kreatech Diagnostics and researchers from Semmelweis University in Budapest, Hungary, plan to co-develop biosample handling methods for use with microarrays, and engage in biomarker discovery, Kreatech said last week.

As part of a new agreement between the organizations, Amsterdam-based Kreatech will work with Semmelweis University's Department of Pathology and Experimental Cancer Research. The researchers will design methods that will use Kreatech's Universal Linkage System for labeling to process limited amounts of formalin-fixed, paraffin-embedded samples for use in array comparative genomic hybridization studies.

The resulting micromethods could later be used in biopsies, laser capture of microdissected cells, and fine needle aspiration, Kreatech said.

Additionally, Kreatech will seek to take advantage of Semmelweis University's large tissue repository to define putative biomarkers for certain tumor types, including lung, soft tissue, breast, and neuropathological malignanicies. Kreatech said it will develop and manufacture the corresponding DNA probes for in situ hybridization.

Harald Berninger, Kreatech's vice president of sales and marketing, told BioArray News this week that the deal with Semmelweis is one of several diagnostic partnerships in which the Dutch firm is engaged. Kreatech is in contact with "various partners in Europe focused on the launch of clinical relevant tests," he said. "As a small company it is very important for us to establish these kinds of collaborations." He declined to disclose the identity of Kreatech's other partners.

Kreatech's core technology is its Universal Linkage System, an enzyme-free labeling method that couples a monofunctional platinum complex to a detectable molecule of choice, such as DNA, RNA, or protein. Traditionally, the company's customers have used the ULS kits for comparative genomic hybridization, miRNA, and gene-expression studies, and have used its ULS-powered FISHBright labeling kits for fluorescent in situ hybridization applications.

In 2007, though, Kreatech Biotechnology rebranded itself Kreatech Diagnostics and has since put itself on the path to being a one-stop-shop for molecular cytogeneticists (see BAN 2/3/2009).

According to Berninger, the goal of the Semmelweis collaboration is develop a clinical application for array CGH.

"Array CGH today still is mostly used as a research tool, which limits its dissemination," Berninger said. "We believe the really interesting potential in this method lies in being able to use it for diagnostics on patient samples, which is compromised due to the difficulties employing array CGH for low amounts of FFPE samples."

There are currently several challenges to running CGH experiments on FFPE samples, including degradation of sample material, which interferes with labeling; the bias that is introduced by performing whole-genome amplification on a sample; and the use of enzyme-based labeling methods, all of which Berninger said can introduce further bias.

In the project with Semmelweis University, Kreatech plans to use limited amounts of genomic DNA isolated from FFPE samples that will be subjected to amplification and ULS labeling. As Semmelweis has an extended FFPE library plus the matching fresh frozen samples with known array CGH profiles, the partnership is the "ideal surrounding for determining the best amplification technology that in combination with the ULS labeling technology will introduce the least bias when only very low amounts of genomic DNA from FFPE samples is available for array CGH analysis," Berninger said.

Beyond developing the new methodology, though, is the potential for Kreatech and Semmelweis to develop diagnostic assays of their own. Zsofia Balogh, a researcher at Semmelweis' 1st Department of Pathology and Experimental Cancer Research, told BioArray News this week that her department is the reference Hungarian center for hematological and solid tumor diseases. The university's archived tumor bank covers "a broad area of interest including but not limited to lung cancer, soft tissue, breast, and neuropathological tumors," she said.

Balogh and colleagues started to work with Kreatech's FISH probes in routine hematological, soft tissue tumors and breast cancer diagnostics a year ago, using probes for chronic lymphocytic leukemia, acute myeloid leukemia, acute lymphocytic leukemia, and breast cancer. Balogh said she has also used Kreatech kits to validate CGH results by FISH and to use ULS to label challenging samples for downstream microarray analysis.

"We have common interests in developing tools for molecular cytogenetics, which we can better tackle if we team up together," said Berninger of the partnership. "We would bring in certain technology and manufacturing know-how, and Semmelweis would contribute by its availability of patient samples and expertise in interpreting results on clinical samples. "How Kreatech and partners will proceed following discovery depends on the nature of the biomarker," Berninger said.

"In case candidate genes are identified as being amplified or overexpressed in specific tumors, such amplifications can directly be visualized with a gene-specific FISH probe," he said. "With our design expertise at Kreatech in the field of FISH, we could then manufacture such a DNA probe that may have the potential to become part of a diagnostic test in conjunction with a drug that may be prescribed depending on the amplification state of this specific biomarker," he added.