Inside Stanford Medicine - June 4, 2012 - by Andrew Myers
Stephen Quake, PhD, a professor of bioengineering and of applied physics at Stanford University and an investigator for the Howard Hughes Medical Institute, has been named the 2012 winner of the $500,000 Lemelson-MIT Prize.
Holder of over 80 patents, founder of at least four companies based on his conceptions and inventor of technologies that have transformed science and medicine, Quake does work that cuts across a diverse array of fields, such as genomic sequencing, microfluidics, immunology, infectious disease and medical diagnostics. His innovations include a rapid DNA sequencer, a non-invasive prenatal test for Down syndrome and the biological equivalent of the integrated circuit.
“We are thrilled to honor Steve Quake, whose groundbreaking work in the field of molecular measurement has created new devices and technologies that will contribute to improving health,” said Dorothy Lemelson, chair of The Lemelson Foundation, a private philanthropy that funds the Lemelson-MIT Program. “Stephen has also been a pioneer in inventing new tools that will allow others to engage in scientific discovery and the prototyping of new biomedical devices quicker and easier, paving the way for even more breakthrough ideas.”
Quake is one of an emerging class of scientists in the burgeoning discipline of bioengineering, which seeks to fuse engineering and life sciences to promote scientific discovery and the development of new technologies and therapies in human health and environmental sustainability.
Quake is one of an emerging class of scientists in the burgeoning discipline of bioengineering, which seeks to fuse engineering and life sciences to promote scientific discovery and the development of new technologies and therapies in human health and environmental sustainability. Stanford’s Department of Bioengineering is a collaboration of the School of Engineering and the School of Medicine. Established in 2003, it is the university’s newest department. Quake serves as its co-chair.
“I’ve never been satisfied to just publish a paper and leave it at that. I try to turn these ideas into inventions and companies so the research can change people’s lives,” Quake said. “As a physicist, I’m interested in basic science and in measuring things and this turns out to have important applications in medicine.”
Stanford recognized Quake’s potential early on. “My wife Jean discovered how much promise Steve had in her role as Dean of Admissions,” said Nobel laureate and U.S. Secretary of Energy Steven Chu, who was then a professor in the physics department. “She wrote on the admission file, ‘The Physics Department will love this guy!’”
Chu recalled first encountering Quake in an honors freshman physics class he was teaching, and they became even better acquainted when Quake worked in Chu’s lab in his junior and senior years. During this time, Quake made the first single molecule measurements of DNA elasticity with optical tweezers, Chu said. For this work, Quake was awarded the Apker Prize for the best senior physics thesis in the country.
“I was in awe over how fast he could grasp new ideas and apply his extensive command of mathematics,” Chu said. “I was a total novice in polymer physics, and we taught ourselves and each other. He had a fearless approach to his laboratory work that one person in my group thought was like the proverbial bull in a china shop. Dishes were broken, but things happened — and I loved it.”
After graduating from Stanford, Quake went to Oxford as a Marshall Scholar with the intent of studying string theory, but returned to the molecular strings he studied at Stanford. He earned his doctorate combining the polymer theory he mastered at Oxford with experiments he did in Chu’s lab during his final year as an Oxford student. After Oxford, he spent another two years in Chu’s lab further developing his experimental skills, Chu said.
Quake explained that early in his career he had watched students in the lab pipetting fluids over and over, and he wondered if there might be a better approach.
“I was looking for a more physics-like way to do this time-consuming work,” said Quake. The result was the biological equivalent of the integrated circuit, with tiny pumps and valves processing fluids rather than data. It is based on the science of microfluidics.
Microfluidics is the study of the behavior and the engineered control of fluids confined to very small volumes — at the “nanoliter” scale, said Quake.
Quake and his colleagues have created chips that integrate thousands of micromechanical valves to allow an unprecedented level of control of biological contents, sometimes leading to experiments that cannot be duplicated on the lab bench.
Quake co-founded a company, Fluidigm, to commercialize his invention, and it now employs more than 150 people.
More recently, Quake made headlines with a rapid and less-costly genome sequencer. He sequenced his own genome for just $50,000 and the help of two lab assistants at a time when, just a year earlier, complete sequences required 200 people and five times the funding. Quake was just the third or fourth person on the planet to see his own genome, and it produced a research paper in which Quake and his doctors evaluated his entire genetic heritage.
“Looking at one’s own genome gives you goose bumps. Your past and future are there before your eyes. Everyone’s got a few skeletons in their genetic closets,” Quake said of his experience.
As he was to become a father, Quake wondered if there was a less-risky way than amniocentesis to test fetuses in uterofor Down syndrome and other chromosomal abnormalities. That thought led to a non-invasive prenatal test for the disease that is as easy as taking a few drops of blood from an expectant mother and testing the little strands of the child’s DNA that make it into her bloodstream. Quake is now using a related approach to provide tests that can determine earlier and more easily whether a transplant recipient’s immune system is at risk of rejecting a donated organ.
“A tissue transplant is really a genome transplant. There’s a little bit of the donor DNA in the blood of the host. We can test and measure this to evaluate how well the recipient is doing,” he explained. At present, organ recipients have to undergo repeated intrusive biopsies to get such an assessment.
Quake’s latest direction is in immunology, a research interest driven by his daughter’s food allergies.
“In the fields of biophysics, micro-fluidics, oncology, prenatal health, and bio-informatics, Steve Quake is almost unique in his breadth of contributions and influence,” said Chu. “His continuous stream of inventions of new methods and instrumentation is having enormous impact.”
Quake also is responsible for establishing a microfluidics center at Stanford, and he has provided advice and assistance to the Department of Energy’s Joint Genome Institute.
“Steve Quake is the most remarkable inventor I have ever had the pleasure to work with closely,” said Stanford colleague and chair of bioengineering Russ Altman, MD, PhD. “While co-chair, he has — ‘on the side’ — advanced science and technology over a broad array of areas. The discoveries are diverse, but the modus operandi is clear: Steve dives deeply into unsolved problems to understand the technical challenges. He then uses his profound knowledge of physics, biology and engineering to devise solutions, and creates and leads teams that can implement his vision and get things to work. He does this time after time.”
Jim Plummer, PhD, dean of the Stanford School of Engineering, added, “It is important to remember that, at just 43 years old, Steve Quake has introduced a number of inventions, any one of which most people would consider a lifetime achievement — and there’s more to come. The true measure of the man, however, is less in his remarkable productivity, but in the profound reach of his inventions. The world is a better and healthier place because of the inventions of Stephen Quake. Stanford is honored to call him one of our own. The Lemelson Prize is well-deserved.”
Asked what the Lemelson-MIT Prize means to him, Quake turned reflective. “This is quite humbling — especially because I’ve never considered myself an ‘inventor’ per se. It’s hard to be singled out, since these inventions are all the result of tremendous collaborations. I have incredible colleagues and I've been privileged to work with many talented students and postdocs. And, of course, none of the commercialization would have happened without a lot of people working very hard at the various companies we’ve created,” Quake said.
“I consider him to be a national — really a global — treasure,” said Altman. “We are incredibly proud of the Lemelson-MIT Prize for Steve, and are confident that he will continue to be a source of productive and high-impact innovation for years to come.”