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Thursday October 30, 2014

Battling Cancer with Big Data

Battling Cancer with Big Data

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Rutgers collaboration demonstrates the promise of precision medicine

Ganeshan, Parashar, Foran
Photo: Jody Somers
Shridar Ganesan, Manish Parashar and David Foran are helping shape a revolution in how best to determine cancer therapy.

Together, three Rutgers entities – the Cancer Institute of New Jersey, the Discovery Informatics Institute (RDI2) and RUCDR Infinite Biologics – form a collective powerhouse with an enhanced capability to unlock the genetic mysteries of cancer.

One Rutgers, A World of Discovery

The new Rutgers, combining nearly 250 years of academic excellence with a renewed commitment to medical education, is inspiring faculty, students and staff to form innovative partnerships in academic research and public service. In an online series, Rutgers Today examines the new ways that members of the university community are collaborating, across a wide range of disciplines, to better meet the needs of the people of New Jersey and beyond.

– The Editors

Throughout most of human history, a cancer diagnosis was considered a death sentence – a fatal forecast of physical deterioration as mutant cells aggressively attacked the victim’s body.

One of the most significant recent breakthroughs in the war on cancer is the rise of precision medicine, the painstaking process of identifying the tiniest molecular and genomic details within a cancer, then using those details to fine-tune treatment. 

An explosion in knowledge about the genetic mutations that cause tumors allows physicians to pinpoint DNA changes that drive cancer cells and tailor treatments faster and more confidently, based on each patient's genetic profile.

“What we have learned through the years is that cancer is not a single disease, but rather a collection of diseases, each with unique features,” says Shridar Ganesan, associate director for translational science at Rutgers Cancer Institute of New Jersey and associate professor of medicine at Rutgers Robert Wood Johnson Medical School

“Instead of determining cancer type only by the organ in which it originates, time-saving genomic analysis opens the door for additional classification by the set of changes present in each cancer, which can guide more precise, or tailored, therapy,” notes Ganesan, who is also a medical oncologist.

Despite these advances, cancer treatment remains a race against time – a struggle to find the best way to beat the disease.

Enter Big Data.

Aided by supercomputing resources, Rutgers doctors and scientists are analyzing genomes and human tissues – and identifying cancer patterns – far faster than ever before.

This novel approach to cancer diagnosis and treatment teams physicians, scientists, pathologists, geneticists, systems biologists and others from the Cancer Institute with computer engineering experts at the Rutgers Discovery Informatics Institute (RDI2). Enhancing the relationship further is collaboration with another university entity – RUCDR Infinite Biologics, the world’s largest university-based biorepository, located within the Human Genetics Institute of New Jersey.  

“We have the latest technology to come up with potential solutions very fast,” says Manish Parashar, director of RDI2 and a professor in the Rutgers School of Engineering’s Department of Electrical and Computer Engineering

The scientists at RDI2 receive patient tissue samples from the Cancer Institute that have been digitized at high resolution, and work closely with the institute’s medical-imaging experts to understand the computational and data challenges and come up with a treatment plan.

“Our team provides the computational engine to review thousands of images, so our collaborators at the Cancer Institute can analyze these images, search the database, test hypotheses and answer important questions,” Parashar says. “We take the imaged samples and radiology studies from one patient and ask, ’Have I seen a case like this before?' ”

By optimizing the data-mining and pattern matching algorithms developed by a research team led by David J. Foran, bioinformatics executive director at the Cancer Institute, the software can be run in a high-performance computing environment. “That way the analysis can be completed in a matter of minutes, rather than days, ” Parashar says.  

Data crunching and analytics expertise provided by RDI2, and biomaterials and technical support from RUCDR Infinite Biologics – coupled with evaluation by a team of scientific, clinical and bioinformatics experts at the Cancer Institute – are shaping a revolution in how best to determine therapy – a vast improvement over the time-intensive, trial-and-error approach that clinicians have faced for years.  

While other U.S. cancer centers engage precision medicine experts to target the more common breast and prostate cancers, the Cancer Institute at Rutgers is believed to be one of the few centers addressing the challenges of rare and poor-prognosis cancers – such as ovarian cancers, pancreatic cancers, sarcomas and certain pediatric cancers – for which traditional therapies usually don’t work. A clinical trial there is focused on the genomic makeup of a tumor, offering hope to poor-prognosis patients.

One Patient's Story

Kevin Touhey of Medford, New Jersey, is one of the people benefiting from the advances of precision medicine. A former basketball coach at the University of Pennsylvania turned life coach and motivational speaker, Touhey arrived at the Cancer Institute in early 2013 with Stage IV lung cancer.

“Never having smoked a cigarette in my life, I was shocked this would happen to me,” Touhey said.

Because of his history, physicians suspected Touhey had a genetic mutation that might respond to a targeted treatment. An analysis of his identified a genetic variation that tends to respond to an anticancer drug designed to target that mutation. Within three days of taking the drug, available in pill form, Touhey’s persistent cough and pain receded.

“I went from walking slowly across my living room to walking distances of 50 yards at a time without feeling out of breath,” Touhey said. He also was able to quickly resume his more strenuous activities, like trampoline workouts and body surfing.

Potential to Spur New Partnerships

New agents to target genomic mutations like Touhey’s are being developed at a very rapid rate, thanks to collaborations such as those between the Cancer Institute. RDI2 and RUCDR Infinite Biologics.

The partnership between the Cancer Institute and RDI2 evolved from joint projects over several years, while Cancer Institute investigators have benefited from research sequencing capabilities from RUCDR Infinite Biologics since 2012. The collaborations grew even stronger as Rutgers prepared to integrate in July 2013 with the Cancer Institute and most of the other schools, centers and institutes that made up the former University of Medicine and Dentistry of New Jersey.

Such an enriched research environment is conducive to groundbreaking discoveries and new treatment options – allowing New Jerseyans to remain close to home to receive the most advanced cancer care. 

 “Joining forces and areas of expertise offers Rutgers the opportunity to develop customized approaches for extracting genomic information from tumors, interpret the genomic variation and offer options to patients that may not be available elsewhere,” says Jay A. Tischfield, scientific director and CEO of RUCDR Infinite Biologics. In addition, the enhanced collaboration has the potential to spur new partnerships with pharmaceutical and biotechnology companies and additional grant-funding opportunities.

This initiative also provides an opportunity to invest in the future of the precision medicine field, enabling students from Robert Wood Johnson Medical School and the School of Engineering to work together, Parashar says. “This allows them to talk to both sides: precision medicine pathology and the radiology side, as well as the computer science and computer engineering side.

“That’s one of the key goals – getting students equipped with the necessary multidisciplinary skills that combine understanding how to deal with Big Data and understanding the science you want to do with it,” Parashar says.


Click here to read other articles in the One Rutgers, A World of Discovery series.

 

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