New center to advance genomic analyses to guide personalized medical care

Michael Snyder

Medicine will never be the same.

That’s the consensus of researchers and physicians at the Stanford University School of Medicine who are familiar with whole-genome sequencing and its coming impact on clinical care recommendations. And it’s not just for genetic pioneers — such as bioengineering professor Stephen Quake, PhD, who last month made front-page news when his entire genome was publicly scrutinized — but for everyday people like you and me.

“I can envision a day that every person who walks into Stanford Hospital & Clinics can, if they choose to do so, have their entire genome sequenced to aid in the diagnosis and treatment of their unique conditions and disorders,” said Michael Snyder, PhD, the Stanford W. Ascherman, MD, FACS, Professor in Genetics.

That day may well come before you realize. The cost of such sequencing is dropping rapidly, said Snyder, and will approach a mere $1,000 per person within the next two years.

He should know. Snyder, who chairs the Department of Genetics in the medical school, is the director of Stanford’s new Center for Genomics and Personalized Medicine. The center blends highly efficient, rapid sequencing technology with the research and clinical efforts of experts in genomics, bioinformatics, molecular genetic pathology and even ethics and genetic counseling to bring advances from the laboratory to the patient.

“Our intention is to integrate genomics information with every aspect of medicine,” said Snyder, who is also a member of Stanford’s Cancer Center. “The center will allow us to do this on an unprecedented scale.”

The medical school is uniquely positioned for such an endeavor, Snyder believes. The close collaboration between basic scientists and clinical researchers at the university, coupled with the nearby technological hothouse of Silicon Valley, ensures continued innovation in both sequencing equipment and data interpretation software.

“The incredible pace of innovations and technical advances in sequencing the human genome more rapidly and cheaply heralds the prospect of predicting the risk for many diseases that occur throughout the human life cycle; for assessing their response to current therapies and the prospect of future interventions; and for monitoring the potential side effects from drugs on a personalized basis,” said medical school dean Philip Pizzo, MD. “Stanford has been a leader in genetics and genomics for decades, and is now poised to help further transform the diagnosis, treatment and prevention of human disease through its Center for Genomics and Personalized Medicine.”

“Genomics and personalized medicine clearly represent a critical component of the future of pathology,” agreed Stephen Galli, MD, professor and chair of pathology and co-director of the Center for Genomics and Personalized Medicine. “Pathology is currently responsible for diagnosing genetic abnormalities ‘one gene at a time,’ typically to identify the genetic basis of disorders already evident in the patient. By analyzing the subject’s entire genome, and advancing our understanding of how to use such information in a clinically appropriate way, we will be able to catalyze the transition in medicine from the current ‘diagnose and treat’ model of care to an exciting new model that includes the ability to ‘predict and prevent.’” Galli is also the Mary Hewitt Loveless, MD Professor in the School of Medicine, as well as a member of Stanford’s Cancer Center, the Institute for Immunology, Transplantation and Infectious Disease, and Bio-X.

The center’s sequencing facility on California Avenue is already up and running with machines using the latest technology, said Snyder, who estimates the new equipment increases the facility’s sequencing capacity by about fivefold while also significantly reducing the cost.

However, not everyone will need to have his or her genome completely sequenced to benefit from the new relationship between genetics and medicine. Databases like the Stanford-managed Pharmacogenetics and Pharmacogenomics Knowledge Base, or PharmGKB, directed by Russ Altman, MD, PhD, who co-chairs the bioengineering department, will allow physicians to make prescribing and dosing decisions about common medications based on genetic variation in specific regions of the genome.

And advances in sequencing blood and tissue samples will allow physicians to measure and incorporate information about many more variables in medical decision making. “Right now physicians typically assess about 10 to 20 different components in a blood draw,” said Snyder. “But with advances in sequencing, we now we have the potential to measure hundreds of thousands of genes.”

Clearly it’s a whole new world, and centers like this one are needed to navigate the murky but exciting waters ahead. For instance, clinicians are going to need to learn how to understand and incorporate unimaginable amounts of genetic data into their analysis of a patient’s health and any recommendations they may make.

“Technology has advanced to the point to where the biggest bottleneck in moving forward is not going to be sequencing whole genomes, but will move instead to the interpretation of the resulting data,” said Snyder, who pointed out that a recent analysis of Quake’s genome, which is the first of its kind to provide a comprehensive overview of disease risks based on the genetic information, involved many of the same experts who will be part of the new center.

Atul Butte, MD, PhD, assistant professor of bioinformatics, was part of the effort to translate information in Quake’s genome into concrete clinical recommendations. His team members not only categorized thousands of genetic variations associated with specific disorders, they also worked to relate that genetic risk to environmental triggers. For instance, Quake’s higher risk for cardiovascular disease could mean that he should avoid smoking and get more exercise — common suggestions that gain urgency in a genetic background such as Quake’s. Recently, Butte also devised a way to analyze previously existing databases of human health and exposure to identify unknown relationships between type-2 diabetes and environmental pollutants.

It’s evident that, unlike many other centers at Stanford and elsewhere that focus on a specific disorder, such as cancer or a group of organs like the cardiovascular system, the Center for Genomics and Personalized Medicine will advance our understanding of many human diseases. After all, there’s no escaping the effect of genes on all aspects of your personal health.

“Our aim is to eventually have everyone diagnosed and treated within the context of their unique genetic background,” said Snyder. “It will change the way medicine is practiced in the future.”