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Together again against prostate
cancer
October 2011
EDIT CONNECT
SHARING OPTIONS:
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 Back |
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