Together again against prostate cancer
October 2011
by Jeffrey Bouley  |  Email the author


MUNICH, Germany—Genomatix Software recently entered into a Cooperative Research and Development Agreement (CRADA) with the Uniformed Service University of the Health Sciences (USU) and the Henry M. Jackson Foundation for the Advancement of Military Medicine to undertake a joint research effort that will seek to differentiate prostate cancer patients with favorable versus poor prognosis at the time of diagnosis and primary treatment using definitive genetic markers discovered through the use of next-generation sequencing (NGS) technology.  
As the parties in the CRADA note, the majority of prostate cancer cases in those people screened via prostate-specific antigen tests fall into a "gray zone" of prostate cancer in which outcomes are extremely difficult to predict at the time of diagnosis. The collaboration will combine the translational research resources of the USU's Center for Prostrate Disease Research (CPDR) with Genomatix's data analysis expertise in, as Genomatix founder Dr. Thomas Werner puts it, "teasing out novel androgen receptor binding sites in the genome and analyzing prostate cancer metastasis using prostate cancer model systems and clinical specimens."  
Werner maintains that Genomatix is one of the world's leading suppliers of technologies to analyze and interpret genomic data and notes that "as well as laying the groundwork for microarray experiments and NGS data analyses, our hardware and software solutions help answer the typical questions posed by systems biology."  
All of this fuels the company's stated approach to research, which is to combine multiple lines of evidence to perform an integrated meta-analysis.  
This isn't the first time Genomatix and USU's CPDR have worked together. In fact, their substantive work goes back to the early 2000s, having conducted research leading to two key publications: "Androgen receptor binding sites identified by a GREF_GATA model" in 2005 in the Journal of Molecular Biology and "Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens" in 2007 in the journal Prostate Cancer and Prostatic Diseases
"This CRADA is a natural extension of accomplishments we have already achieved together," Werner says. "Next-generation sequencing opens a new dimension in biomarker research and will allow a finer grained, unbiased look at some of the genomic mechanisms behind prostate disease, thus providing the opportunity for the discovery of new prognostic biomarkers, some of which also may be targets for therapeutic intervention and treatment monitoring."
Dr. Shiv Srivastava, the CPDR's co-director and scientific director, as well as a professor of surgery at USU, agrees that USU and Genomatix work well together, noting, "our work to date with Genomatix has been very productive. People from both our organizations have already established quality working relationships. Leveraging this and moving forward together into a technology as groundbreaking as next-generation sequencing holds great promise for significant progress in prostate disease research."  
As Genomatix notes on its website with regard to its scientific publications, "Research has always been and always will be the driving force behind daily work at Genomatix. It's the engine that propels fundamental advances in biology and medicine. Our know-how helps keep this motor running and—wherever we can—make it even more powerful than it is today."  
Work such as this is expected to help advance Genomatix's goal to find more meaningful answers to biology's fundamental questions by focusing on gene regulation and gene expression, and the work of the CRADA fits in with the company's stated vision of being built of the three pillars of better diagnoses, better prognoses, better therapies, with an eye toward helping to usher in an era of personalized medicine.  
In their 2005 article, Genomatix and the CPDR found that a complex model combing the glucocorticoid responsive element matrix family (GREF) and GATA transcription factor binding sites could be more predictive than GATA alone by recognizing transcription factor binding sites in their proper biological and functional context.  
In their 2007 article, they noted that formalin-fixed paraffin-embedded (FFPE) prostate specimens are rich sources of molecular pathological information, but noted that FFPE-based microarray analysis of tissue samples may be hampered by the degradation and chemical alteration of RNA molecules due to the preservation procedure. To get around this problem, they used probe analyses of Affymetrix oligonucleotide arrays at individual probe level to compensate for the potential loss of gene identifications associated with compromised mRNA quality in FFPE preparations and used laser capture microdissection of prostate tumor and benign epithelial cells. They concluded it was quite possible that a combination of laser capture dissection with computational enhancement of microarray data might be useful for the assessment of gene expression changes in FFPE prostate cancer specimens.

Genomatix launches secure cloud-like model for next-gen sequencing data analysis
MUNICH, Germany—In other next-generation sequencing (NGS) news at Genomatix Software, the company announced in mid-March the launch of a new service, mygenomatix, said to "incorporate all the power of its in-house platform and combine it with the affordability of cloud computing and the security of an in-house solution."
Genomatix says the service will return analyzed data back in a matter of one to two weeks and grant users access to the full Genomatix software and background data content as part of the service. For ease of use, the service uses graphical user interface and standard operating procedures and workflows, and access to software and data content is possible via any standard Internet browser.
"We want to provide an easy entry to our excellent NGS data analysis and interpretation capabilities, complementing our turn-key in-house platforms, the Genomatix Mining Station and the Genomatix Genome Analyzer," said Genomatix CEO Dr. Martin Seifert at the time. "We have been exploring a cloud- like model for quite some time, and our service model addresses the issue of security by getting the data to our computers via a hard disk shipment program. With mygenomatix, anyone doing NGS data analysis now has access to an easy entry path to our technology and databases."
Code: E101116

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