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Data Deluge

Promise - Fall 2011

Bioinformatics Corrals Information Overload to Create Blueprint for Personalized Cancer Medicine

By Dawn Dorsey

Thanks to rapidly advancing technology and groundbreaking research, the past few years have brought fast and furious progress to understanding the molecules that make up the human body.

But the flip side of this phenomenal race is that it’s produced data so quickly that researchers are looking to technology to help them optimize results.

With laboratories generating an 
overwhelming amount of biological
data that could hold the key to 
personalized therapies, it's 
understandable that John Weinstein, 
M.D., Ph.D., often finds himself 
wrapped up in his work.
Photo by John Everett

As discoveries continue to mushroom, scientists are scrambling to find ways to scrutinize data and bring it into the “real world” to help predict, prevent and treat disease. MD Anderson’s Department of Bioinformatics and Computational Biology is at the forefront of learning to translate and use this flurry of information to move closer to a personalized approach to cancer.

“Some people thought sequencing the human genome was an end in itself,” says John Weinstein, M.D., Ph.D., professor and chair of the department. “And it was. But it was just the beginning. There’s been an explosion of data about the body’s genes, proteins and other molecules.  For the first time in medical history we’re generating biological information in the laboratory faster than we can analyze or interpret it on our computers.”

Navigating a universe of data

The scientific discipline called bioinformatics uses customized statistical approaches and supercomputers to relieve the bottleneck caused by quickly escalating discovery. Leading-edge techniques and technologies enable highly trained experts to sift through genetic data searching for information on how to design cancer prevention, diagnosis and treatment plans based on each person’s unique molecular makeup. The scientific niche is built on four pillars of expertise: biology, statistics, clinical medicine and computer science.

“The bottom line of bioinformatics at MD Anderson is learning how to personalize cancer medicine,” Weinstein says. “If we can generate molecular portraits of cancer, we’ll be more able to choose the right therapy for each patient or, better yet, prevent cancers from developing in the first place.”

Weinstein paints a striking visual picture to show the mind-boggling possibilities and the incredible numbers of molecular components in human biology.

“Stretched end to end, the DNA in a single human’s body would circle the equator 455,000 times, the equivalent of 60 round trips to the sun,” he says. “One mistake ― a mutation ― at an unlucky spot anywhere in that length can lead to cancer. Our challenge is to understand how mutations and other genomic aberrations happen so we can try to prevent them and know what to do about them if we can’t.”

Leading, collaborating, discovering

One of the pioneers of molecular profiling for personalized cancer therapy, Weinstein has a personal stake in cancer research. His mother, his grandmother and a number of close friends have died from the disease. MD Anderson recruited the renowned scholar, investigator and inventor in 2008 from the National Cancer Institute, where he had spent more than three decades. His 260 publications include 11 as first author in the prestigious journal Science.

Since Weinstein’s arrival, the department has grown rapidly in response to 
MD Anderson’s expanding needs. In the past two years, it has successfully recruited eight young star faculty members from top institutions around the country, as well as more than two dozen analysts, computer scientists and fellows to support research throughout the institution.

Almost two decades ago, John Weinstein, 
M.D., Ph.D., introduced a way to reduce 
the masses of molecular data to 
something humans can visualize: a 
compact, color-coded clustered heat 
map. One of his early heat maps, 
published in the journal Science, 
reduced 28 feet of almost microscopic 
print on the relationship between genes 
and drugs.

In 2009-2010, the analysts provided bioinformatics support for more than 400 research projects of more than 150 principal investigators in more than 40 MD Anderson departments. Already well on the way to developing international respect for the program, the team received a five-year, $8.3 million grant from the federally funded Cancer Genome Atlas in 2009. 

Private philanthropy is playing a significant role to support bioinformatics and computational biology at the institution, thereby helping advance a better understanding of cancer and the ability to control it. The H.A. and Mary K. Chapman Charitable Foundations, two charitable entities established in memory of philanthropists Mary and Allen Chapman of Tulsa, Okla., made a generous gift of $1.75 million to support the Chapman Fund for Bioinformatics in Personalized Cancer Therapy under Weinstein’s direction.  

The bioinformatics program also has received an anonymous gift of $250,000 as well as numerous smaller donations. Most recently, the Michael & Susan Dell Foundation committed a $2.5 million grant in honor of Michael Dell’s mother, MD Anderson Board of Visitors member Lorraine Dell of Houston. The Lorraine Dell Program in Bioinformatics for the Personalization of Cancer Medicine will build a fully equipped, multidisciplinary team devoted to analyzing and interpreting molecular profiles.

Stepping away from their computers and labs, statistical analysts in the department collaborate closely with clinical and basic science researchers in many areas across MD Anderson. They work side by side with biomedical scientists and clinicians to determine efficient and effective approaches to exploring the new data generated every day. The analysts lend valuable expertise, helping colleagues with grant submissions and data analyses, answering researchers’ questions and discussing issues during weekly drop-in clinics.

A future paved with potential

Moving forward, the department will continue to investigate new ways to design and use computer technology to interpret research. By building collaborations within MD Anderson and the broader research community, departmental scientists will expand their knowledge and learn to identify the important questions to ask when examining the torrents of data. And, they’ll continue to develop their expertise by sharing knowledge with graduate students, bioinformatics trainees, biomedical scientists and clinicians.

Weinstein sees exciting potential for MD Anderson to take giant steps toward eliminating cancer by learning to leverage the tremendous level of research at the institution.

“With the largest, most vigorous and most honored clinical cancer research program in the world, MD Anderson is uniquely positioned to seize this opportunity and make major advances in personalized cancer therapy,” he says. “Our research provides an engine for progress against cancer that’s simply unmatched anywhere in the world.”

© 2015 The University of Texas MD Anderson Cancer Center