Together again against prostate cancer

Genomatix and Uniformed Service University build on previous work to seek prognostic genetic markers through next-gen sequencing

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MUNICH, Germany—Genomatix Software recently entered into aCooperative Research and Development Agreement (CRADA) with the UniformedService University of the Health Sciences (USU) and the Henry M. JacksonFoundation for the Advancement of Military Medicine to undertake a jointresearch effort that will seek to differentiate prostate cancer patients withfavorable versus poor prognosis at the time of diagnosis and primary treatmentusing definitive genetic markers discovered through the use of next-generationsequencing (NGS) technology.
As the parties in the CRADA note, the majority of prostatecancer cases in those people screened via prostate-specific antigen tests fallinto a "gray zone" of prostate cancer in which outcomes are extremely difficultto predict at the time of diagnosis. The collaboration will combine thetranslational research resources of the USU's Center for Prostrate DiseaseResearch (CPDR) with Genomatix's data analysis expertise in, as Genomatixfounder Dr. Thomas Werner puts it, "teasing out novel androgen receptor bindingsites in the genome and analyzing prostate cancer metastasis using prostatecancer model systems and clinical specimens."
Werner maintains that Genomatix is one of the world'sleading suppliers of technologies to analyze and interpret genomic data andnotes that "as well as laying the groundwork for microarray experiments and NGSdata analyses, our hardware and software solutions help answer the typicalquestions 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 integratedmeta-analysis.
This isn't the first time Genomatix and USU's CPDR haveworked together. In fact, their substantive work goes back to the early 2000s,having conducted research leading to two key publications: "Androgen receptorbinding sites identified by a GREF_GATA model" in 2005 in the Journal ofMolecular Biology and "Transcriptomeanalyses of benign and malignant prostate epithelial cells in formalin-fixedparaffin-embedded whole-mounted radical prostatectomy specimens" in 2007 in thejournal Prostate Cancer and Prostatic Diseases
"This CRADA is a natural extension of accomplishmentswe have already achieved together," Werner says. "Next-generationsequencing opens a new dimension in biomarker research and will allow a finergrained, unbiased look at some of the genomic mechanisms behind prostatedisease, thus providing the opportunity for the discovery of new prognosticbiomarkers, some of which also may be targets for therapeutic intervention andtreatment monitoring."
Dr. Shiv Srivastava, the CPDR's co-director and scientificdirector, as well as a professor of surgery at USU, agrees that USU andGenomatix work well together, noting, "our work to date with Genomatix has beenvery productive. People from both our organizations have already establishedquality working relationships. Leveraging this and moving forward together intoa technology as groundbreaking as next-generation sequencing holds greatpromise for significant progress in prostate disease research."
As Genomatix notes on its website with regard to itsscientific publications, "Research has always been and always will be thedriving force behind daily work at Genomatix. It's the engine that propelsfundamental advances in biology and medicine. Our know-how helps keep thismotor running and—wherever we can—make it even more powerful than it is today."
Work such as this is expected to help advance Genomatix'sgoal to find more meaningful answers to biology's fundamental questions byfocusing on gene regulation and gene expression, and the work of the CRADA fitsin with the company's stated vision of being built of the three pillars ofbetter diagnoses, better prognoses, better therapies, with an eye towardhelping to usher in an era of personalized medicine.
In their 2005 article, Genomatix and the CPDR found that acomplex model combing the glucocorticoid responsive element matrix family(GREF) and GATA transcription factor binding sites could be more predictivethan GATA alone by recognizing transcription factor binding sites in theirproper biological and functional context.
In their 2007 article, they noted that formalin-fixedparaffin-embedded (FFPE) prostate specimens are rich sources of molecularpathological information, but noted that FFPE-based microarray analysis of tissuesamples may be hampered by the degradation and chemical alteration of RNAmolecules due to the preservation procedure. To get around this problem, theyused probe analyses of Affymetrix oligonucleotide arrays at individual probelevel to compensate for the potential loss of gene identifications associatedwith compromised mRNA quality in FFPE preparations and used laser capturemicrodissection of prostate tumor and benign epithelial cells. They concludedit was quite possible that a combination of laser capture dissection withcomputational enhancement of microarray data might be useful for the assessmentof gene expression changes in FFPE prostate cancer specimens.

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

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