Center uses computer science to fight cancer

Center
uses computer science to fight cancer

BY MARGOT DIMOND
and NANCY JENSON

Rice University
and The University of Texas M.D. Anderson Cancer Center
are teaming up to combine high-level computer science with
efforts to understand, treat and ultimately prevent cancer.

Using their own
funding, the two universities have created the Gulf Coast
Center for Computational Cancer Research. The center was
formed under the auspices of the Gulf Coast Consortium for
Bioinformatics.

While other cancer
centers around the nation are turning to computer scientists
to assist their investigations, this center is unique in
the scope of projects planned by scientists at Rice and
M.D. Anderson.

For example,
center scientists plan to improve the design of clinical
trials of novel therapies by using computers to simulate
the trials before they begin. Then, as the trial is under
way, real-time data can be collected and analyzed and changes
can be made in the trial design as promising results are
obtained. Such flexibility would offer patients the best
therapies as soon as possible.

The center’s
work will further build on advances in analysis technologies
that enable the assembly of large databases of detailed
profiles of genes and proteins obtained from cancer patients.
These databases will include a broad range of profiles,
beginning with precancerous lesions and continuing to metastasized
tumors through treatment and into remission. Analyzing these
profiles, researchers can identify the specific mutations
that cause different cancers, create tests for each possible
variation and design patient-specific treatments.

“The rapid
advance of technology has created a number of opportunities
for understanding the causes of cancer and its treatment,
but each of these opportunities requires the development
of custom, high-performance software that can run efficiently
on modern supercomputers,” said Ken Kennedy, University
Professor, the Ann and John Doerr Professor in Computational
Engineering in Computer Science, professor in electrical
and computer engineering and co-director of the center.
“At Rice, we have the resources to develop that software,
and we are looking forward to working with M.D. Anderson’s
cancer researchers to meet this critically important challenge.”

High-performance
software is necessary in cancer research because of the
large size of the databases. Cancer is many thousands of
different diseases. For malignancy to occur, a number of
mistakes must become established in the DNA of the descendants
of a single cell. Since these mutations can occur in different
genes, there are vast numbers of possible combinations of
cancer-causing mutations — larger than the number of
atoms in the universe — so even identifying them is
a daunting task, the scientists say.

The center will
both facilitate the development of this software and simplify
the applications to make them more broadly accessible to
cancer researchers.

“Our goal,
of course, is to effectively treat and even prevent cancer,
and with this center, we will be developing more efficient
strategies for deciding how to do that,” said the other
co-director of the center, Donald Berry, professor of biostatistics
and applied mathematics at M.D. Anderson Cancer Center.
“We will apply high-level computing to virtually every
aspect of cancer treatment, from cancer diagnosis and protein
modeling of each patient, to drug discovery and clinical
trial design.

“The computing
needs of the cancer research community are enormous, and
with the intellectual expertise in problem solving offered
by our collaborators from Rice, we can open doors that we
can only now imagine exist,” Berry said.

The Gulf Coast
Consortium for Bioinformatics fosters collaborations among
information technology, computer science, statistics and
biological and medical sciences. It is part of the Gulf
Coast Consortia, a research and education collaboration
of six prominent institutions in the Houston-Galveston area.
The other four partner consortia institutions — Baylor
College of Medicine, University of Houston, The University
of Texas Health Science Center at Houston and The University
of Texas Medical Branch at Galveston — may also participate
in this enterprise.

For more information,
go to <www.gulfcoastconsortia.org>.

—Margot
Dimond is Rice News staff. Nancy Jensen is executive director
of the M.D. Anderson Cancer Center’s Communications
Office.