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Robert B. Darnell, MD, PhD, President and Scientific Director, New York Genome Center

Robert B. Darnell, MD, PhD, President and Scientific Director, New York Genome Center

By Robert B. Darnell, MD, PhD

When I was studying for my PhD in molecular biology in the 1980s, I labored heads-down for a year in a wet lab sequencing 140 base pairs of genes. It was hard work. Today, using the most advanced gene sequencing machines at the New York Genome Center, this year we will sequence 65 million base pairs every second (4 billion every minute). Stunning.

The genetic revolution that began when James Watson and Francis Crick discovered the double-helix structure of DNA in 1953 is racing ahead at a dizzying speed. The epic Human Genome Project in the 1990s mapped the entire genome, giving scientists a much clearer understanding of how the body works. And, over the past decade, gene sequencing machines have made it possible to affordably sequence every base pair in an individual’s entire genome.

But to make this technology truly relevant to human disease, something was missing. There has been a mismatch between the amount of data generated and powerful analytical tools capable of making sense of that vast amount of genetic information—the Big Data of human biology.

So, now comes a new wave of innovation. The New York Genome Center and IBM are working together to harness the power of IBM Watson to help doctors find the patterns that cause diseases and discover the best treatments for individual cancer patients. In this way we are building a foundation that can lead to breakthroughs in how clinical genomics can improve patient care today.

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The New York Genome Center was established in 2011 with the goal of combining the resources of some of the world’s finest hospitals and academic medical centers to create one of the most potent medical genomics institutions in the world. In September 2013, we opened our headquarters in downtown Manhattan, and are eagerly awaiting the arrival of new sequencing machines capable of sequencing an individual’s entire genome in under three days at a base cost of $1,000.

Powered by the unprecedented collaboration of our member organizations, NYGC is generating a new kind of academic institute, focused on a consortium-based approach to tackle technology and use it to generate transformation in how we treat sick patients. We are emerging as a true academic and research institute. We’re setting our agenda and launching projects in collaboration with our network of members, and steering projects and strategies to help change genomic medicine from a concept into a reality. The IBM Watson project is our most ambitious.

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It’s designed to resolve a dilemma: the capabilities of sequencing machines are racing ahead of our ability to usefully harness their output. Clinical trials often last many years and cost many millions of dollars. That’s too slow and too expensive.

This is where Watson plays a role. Our goal is to provide Watson a consistent stream of genomic data, electronic medical records, pharmacological information and medical literature related to an individual patient’s cancer. Together with the NYGC analytics resources of tools and people, we will assess the impact of gene mutations on tumor cells—the cause-and-effect trail of the cancer.

Ajay Royyuru, Director, Computational Biology Center, IBM Research (L), and Dr. Robert B. Darnell, discuss Watson's capabilities.

Ajay Royyuru, Director, Computational Biology Center, IBM Research (L), and Dr. Robert B. Darnell, discuss Watson’s capabilities.

The idea is that oncologists will be able to use Watson as an advisor, helping them to identify an existing drug or drugs that can be repurposed to attack the patient’s cancer. The system provides shortcuts to solutions.

The joint study by NYGC and IBM will initially help oncologists provide personalized assessments for patients with glioblastoma. I have worked as a neuro-oncologist for nearly 25 years, and have empathized with patients and been privately frustrated by our inability to deal effectively with an aggressive brain cancer that kills more than 13,000 people in the United States each year. We have obtained IRB approval to begin a clinical trial, which will involve nine New York area institutions and 20 patients. We hope to learn lessons from taking on glioblastoma that eventually will be useful in addressing many of the more than 100,000 cancer cases that are diagnosed each year in New YorkState alone.

Life sciences are at a turning point. By bringing together the expertise of physicians, pharmacologists, molecular biologists, computer scientists and mathematicians, we can solve complex problems that none of these disciplines can solve individually.

For me, this moment is particularly meaningful. My father, James Darnell, one of the pioneers of RNA research in academia, is my scientific hero. In my education and career I chose a different path. I chose to bridge the worlds of academic science and medical practice.

With the IBM Watson project, we’re doing science that saves lives.

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