Meeting participants at the 6th Future of Genomic Medicine conference in San Diego seemed to be having fun yesterday afternoon. At least it looked that way to observers, like NYGenome contributor Christie Rizk, who followed the meeting via Twitter. Rizk reported on the meeting's first sessions yesterday, and continues her coverage here.
Mount Sinai's Eric Schadt gave a talk Thursday afternoon on how big data benefits patients. But his slide animations got the most attention. He made network biology "look pretty," tweeted Konrad Karczewski, and Alicia Martin called a penalty on Schadt for "excessive use of beautiful visualizations." Appealing visuals aside, Schadt described how knowledge of biological networks could drive the development of cancer drugs, and said identifying genes that regulate those networks could have an impact on disease outcomes.
George Weinstock of Washington University in St. Louis made a splash with his talk about the microbiome, particularly when he spoke about collecting dirty diapers from the WashU NICU in order to sequence the microbiome of newborns, and his work with acne microbes. Microbial sequencing could soon be as cheap as one dollar, Weinstock added, and it's important to identify beneficial bacteria, not just harmful microbes.
As the second day of the conference began today, the focus was on cancer. Siddhartha Mukherjee, author of The Emperor of All Maladies: A Biography of Cancer and a Columbia University professor, said that now that researchers have the capacity to deeply analyze cancer genomes, the question is what to do with that information. The spectrum of mutations within cancer patients' diseases is different, he added, and it's important to ask about the diversity, identity, complexity, and actionability of each. "The end goal should be to treat and cure patients, not get more genomes," Mukherjee said. He called cancer a network-based disease, saying that the entire gene network needs to be targeted in order to treat it.
Washington University in St. Louis' Elaine Mardis talked about what she calls the "Maserati approach" to cancer sequencing — combining whole-genome sequencing, exome sequencing, and transcriptome sequencing to get as much actionable information as possible. RNA sequencing is key, Mardis said, because there are many genes that, while mutated, are not expressed. She agreed with Mukherjee that cancer must be treated based on pathways, not gene signatures. If it becomes obvious that genomics is clinically effective, patients will start to demand it, she added. Mardis is currently putting together a public database of cancer drugs and genes. She is also working on using RNA sequencing to create personalized cancer vaccines, a move Forbes' Matthew Herper tweeted "sounds so tough to commercialize."
Randy Scott, CEO and co-founder of genome sequencing company InVitae, spoke about his firm's efforts to make genome sequencing available to every person on Earth. He compared genetic testing to cell phones: something everyone will soon want. InVitae is offering an assay that tests for 264 diseases for $1,500, and plans to offer testing for 1,000 diseases for $1,000 in 2014. Clinically relevant genetic information needs to be organized better, Scott added, and the databases must be released to the public. Information is valuable when shared, not hoarded, he said, adding that it's time to move away from genetic testing and into "genome management." Comprehensive genome management may be "the job for the doctor of the future," tweeted Steven Tucker. Gholson Lyon tweeted his approval of Scott's open data idea, and he received applause when he suggested an end to gene patents.
Susan Desmond-Hellmann, chancellor of the University of California, San Francisco, got a positive reaction from her audience when she suggested the first step towards precision medicine is to revamp our disease taxonomy to make it more accurate. For example, she asked, why is breast cancer still called breast cancer, and not HER2 cancer? Accuracy and precision won't cure patients, but it's a good place to start, Hellman said, and to make that happen, researchers need to build a knowledge network comparable to Google maps — reliable and updated frequently.
Sanofi's Elias Zerhouni, former director of the NIH, drew attention when he said researchers must accept that they haven't yet successfully simulated human disease, because it's more complex than previously thought. Researchers have also abandoned their focus on disease biology and concentrate too much on animal models, he added. Instead, he suggested a bit of a reversal for disease research — bedside back to bench. Getting genomic data from patients is the key to understanding diseases, and researchers should work backward from the patient to the drug, he said. Following a patient population over time is invaluable, Zerhouni added.
Christie Rizk is a reporter and editor based in New York. She is a regular contributor to the New York Genome Center, and her work has appeared in Genome Technology magazine, Techonomy, Reuters, and The Brooklyn Paper.