Next-Generation Sequencing

career snapshots Next-generation sequencing The speed, cost and accessibility of DNA sequencing has been transformed in recent years by new technologies, opening up exciting possibilities for disease diagnosis and therapeutic intervention. This month, we interview two of the pioneers in the field.

Since then, Branton and Deamer (who is a Branton’s proposal that freeze-etching methods Daniel Branton, Ph.D. professor at the University of California, Irvine, for electron microscopy could reveal the internal Emeritus Professor USA) have continued their research in trying to structure of biological membranes (Science 158, of Biology, Harvard derive sequence information from nanopores, 655; 1967), much to the surprise of experts in University, Boston, and have been joined by many of their students the techniques. “Indeed, following a lecture on Massachusetts, USA. and other investigators. “Although early these results, one expert asked what specialized nanopore experiments disappointed naive facilities I had used,” Branton says. “On hearing expectations of an easy path to inexpensive that we had only some makeshift equipment on In 1991, a conversation with a friend and DNA sequencing, much progress has been a bench-top, he laughed and said: ‘Dan, if you collaborator, David Deamer, about the push to made,” says Branton (see Nature Biotech. had known more about what you were doing, sequence the human genome catalysed Daniel 26, 1146–1153; 2008). “And the advantages you would have realized that you cannot get any Branton’s entry into the field of sequencing of nanopore sequencing — which offer the results doing the experiment the way you did!’” technologies. “Both of us felt that there had prospect of sequencing a mammalian genome Now, together with Jene Golovchenko, to be better ways of undertaking such a giant for ~US$1,000 in ~24 hours — are so attractive Professor of Physics at Harvard, Branton guides sequencing task than with clumsy, slow gels, and that I continue to address the new challenges the research of a group of about 18 people with each of us had alternative suggestions,” recalls in nanopore research.” training in molecular biology, biochemistry, Branton. “But when David proposed driving a Tackling these challenges has taken Branton’s physics, electronics and material science. strand of DNA or RNA through a nanopore to research in many directions, including molecular He finds it particularly rewarding to know that determine how the nucleobases modulated the biology, biochemistry, physics, electronics, their interdisciplinary research could result in ionic current through the pore, we both thought material science and engineering. Consequently, rapid improvements in disease intervention, it might provide an ideal route to sequencing.” he has had to become familiar with many new drug discovery and treatment selection. Having spent much of his career as a cell methods and ways of thinking. “Fortunately, “I also find it thrilling that the notion of biologist (since becoming Professor of Biology at one of my most valuable career experiences sequencing by threading a DNA molecule Harvard in 1973) investigating cell membranes was to learn early on not to be timid about through a membrane channel — an idea that was and their interactions with the cytoskeleton, trying new methods about which I knew little,” at first labelled as ‘wild’ — is now taken seriously Branton thought that trying such experiments says Branton. A collaboration in the 1960s with and is stimulating excellent new science in many would be a refreshing new research endeavour. Deamer demonstrated the applicability of other laboratories,” he concludes.

a graduate student as well: founding CuraGen, For example, the technology was used to Jonathan Rothberg, Ph.D. one of the first genomics companies. sequence the first individual human genome — Chairman, Chief “I wanted to apply what I had learned to health James Watson’s — at a fraction of the cost of Executive Officer, Ion care, but I was in a fantastic lab, and it was the first human genome: $1 million rather Torrent Systems, expected that I would be an academic,” says than $1 billion (Nature 452, 872–876; 2008). Guilford, Connecticut, Rothberg. “Luckily, I discussed starting a company Continuing his drive to develop new USA, and Chairman, with Lynn Jelinski, who ran the biotechnology technologies, Rothberg co-founded RainDance RainDance Technologies, Lexington, centre at Cornell [New York, USA], and she said: Technologies in 2004 to enable miniaturization Massachusetts, USA. ‘Why don’t you just do it?’, and so I did. We wrote of a wide range of laboratory methods. After grants and a business plan for a company that 454 Life Sciences had been acquired by Roche During his undergraduate engineering courses would use computers and sequencing to discover in 2007, he founded Ion Torrent Systems to make at Carnegie Mellon in the mid-1980s, Jonathan drugs based on human genomic information, sequencing accessible to all, by pioneering a Rothberg realized that the decoding of the and we got the funding.” Less then a decade novel approach leveraging a semiconductor human genome was a coming revolution. later, CuraGen had 500 employees and a market device to directly translate chemical “DNA sequencing was unleashing an explosion in capitalization of US$5 billion. CuraGen also sequencing information into digital data understanding, and so I became very interested in published the first global proteomics maps of rather than using light as an intermediary, as in the impact it could have on life sciences,” he says. living organisms and brought some of the first standard methods. “We want high-throughput This started him on the course to founding 454 Life genomics-based drugs into the clinic. sequencing technology to be so low-cost to Sciences, which developed the first commercial In 1999, Rothberg’s career had another key buy and use that it becomes ubiquitous, so we product for next-generation sequencing. turning point. “When my son was born, developed an electronic chip to do it, much like Rothberg was also intrigued by how he was rushed to the intensive care unit. the microprocessor did for computing,” he says. the mind works, and so did his graduate At that moment, I realized I wanted to make Overall, Rothberg emphasizes that it is possible research in molecular biology with Spyros drugs based on an individual’s genome and to pursue outstanding science in industry. “We Artavanis-Tsakonas at Yale, Connecticut, USA, needed to miniaturize sequencing.” On his have demonstrated that you can do influential, where he applied DNA sequencing to discover paternity leave he came up with the ideas and transformational research at companies, a gene called slit that was important in the behind 454 Life Sciences, which developed the from decoding the Neanderthal Genome, to Drosophila melanogaster nervous system. first massively parallel sequencing platform, uncovering what was killing the Honeybee. My But he did something much more unusual for dramatically reducing the cost of sequencing. love is science; I just do it in a different context.”