Big data for better results: the power and the promise of precision medicine

September 26, 2018 | by Sam Lazaryev

Jeffrey Trent Jeff Trent, Ph.D.
City of Hope and Translational Genomics Research Institute (TGen) partnered in 2016 to revolutionize cancer treatment, committing to work together using precision medicine to develop new and better treatments for cancer and other life-threatening conditions.  
 
Here, Jeff Trent, Ph.D., TGen president and research director, discusses the promise of precision medicine and why he's so excited to be working with City of Hope.
 
Q: How do you see precision medicine changing health care?
 
We are seeing a fundamental change in the clinical practice of medicine, particularly in cancer diagnosis and treatment, that is changing patient outcomes and potentially saving lives.
 
With precision medicine, we can now deliver “just-in-time” information about a patient’s unique genetic and biologic characteristics. A physician can make medical decisions based on an understanding of how a specific patient will respond, at the molecular level, to a specific therapy.
 
To put this in historical perspective, in 2006, there were only six personalized medicine treatments and diagnostics in all of medicine. Ten years later, 132 were available. And in 2017, 50 percent of the U.S. Food and Drug Administration’s approvals were for targeted treatments, including the first three personalized immunotherapy treatments. It is not an exaggeration to say that an organization that can fully practice the science of precision medicine has the chance to disrupt the way we treat patients for better outcomes and quality of life.
 
Q: The big data revolution is making vast amounts of information available. How are we harnessing it for precision medicine?
 
I can’t say enough about how remarkable it is to be able to do this. When we sequence a patient’s genome, we are looking at about 100 billion data points. To give you a sense of what that means, an individual’s genome contains about 3 billion data points, but we look at your normal genome and your cancer genome, and compare the two.
 
We have to be accurate, so we sequence the genome about 100 times to make sure we don’t make a single mistake — because a single misspelling of a single letter in the 3 billion letters of your genome will be the determining factor of whether we recommend you get a drug or you don’t get a drug. It literally relies on degrees of accuracy across massive data, which is extraordinary.
 
We are fortunate because TGen partnered with Dell almost a decade ago to build a high-performance computing environment that is tailored to the human genome and delivers data rapidly. It is a massive computer system, one that does about 60 trillion calculations per second. It used to take us months to look at a single genome, and now it takes only a few hours.
 
Why is this important? The ability to perform more computations per month means that we can help more patients, we can understand more about disease and we can do more research. High-performance computing and the advances in understanding data help us deliver the best treatment options to our patients.
 
Q: Why is it so hard to incorporate precision medicine into treatment and why is City of Hope the right place to do so?
 
City of Hope is one of the few institutions worldwide that can actually employ precision medicine.
 
There are three essential elements to effective precision medicine, all of which have to operate at scale. First, we have to provide genetic testing in real time. Second, we have to get ahead of cancer, anticipating how a cancer may evade treatments. And third, it has to have the potential to reduce, not layer on, health care costs.
 
If we do these right, we can have more stories like that of Cheryl Wiers, a mother of two young children, who benefited from chimeric antigen receptor (CAR) T cell therapy. In Wiers’s case, CAR T cells were genetically engineered to target the antigen CD19, a protein found on the surface of non-Hodgkin’s lymphoma and other cancer cells. So far, the treatment combining a stem cell transplant with CAR T therapy has worked for Wiers and other patients.
 
Q: What’s next?
 
We are continuing to use this technology to generate a better understanding of the genome that can help patients. And we are continuing to see remarkable progress as TGen and City of Hope collaborate on the technology and treatment fronts to present outstanding new options to address a variety of cancers.
 
What is important is not just the ability to process data quickly. We want to store, retrieve and analyze the massive amounts of information we are generating on each patient. The combination of the genomic data, tied to clinical outcome data, allows for the development of a “rapid learning system,” which leads us to ask questions such as, “Have we ever seen another patient like this before?”.
 
Finally, the amount of genomic data we work with at TGen today is remarkably large (and will scale exponentially when combining genomic, clinical and imaging data together). Just based on the genomic data available today at TGen, which is in excess of 4 petabytes, it is fascinating to consider just how much information we are working with. 
 
The ability to perform more computations per month using high-performance super-computing, and then capturing and using this data, means we can do more research in one month’s time and, ultimately, help more patients.
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