BUS INESS INSIGHTS
Up From Chaos Clinical experience will bring focus to the data surge of GENOMICS RICK MULLIN, C&EN NORTHEAST NEWS BUREAU
The current glut of data, however, can lay “genius”: Someone who extracts clarity the virtuous circle somewhat flat. “For a lot from chaos and effectively communicates of people, data do become a distraction,” a meaningful vision to the public at large. Quackenbush, who is helping develop a Were we to accept this definition, it would master’s degree program in bioinformatics at serve us well to study the second step in Harvard, told me after the panel discussion. the process. Communication may be what “People substitute our ability, now, to generseparates the true genius from the mere ate large quantities of data for the need to high scorer on standardized tests. intelligently design an experiment.” He sugThis idea of genius has some currency in gested, however, that the participation of the the realm of medicine, where the scientific physician-scientist in drug discovery helps to enterprise has long applied itself to navicounteract the seduction of complex data: It gating the chaos associated with human is much easier to stay focused on the patient disease. In the process, however, science when the patient is in your office, he said. has added layers of human-made chaos And it is much easier to get rid of extraneassociated with research tools and methodous data in the clinic. Jonathan Rothberg, a ologies to the innate chaos found in nature. pioneerinnext-generationgenomesequencAlthough tools and methodologies can lead ing and founder of DNA sequencer supplier to cures, they also can create confusion and Ion Torrent, credits physician-scientists too often distract medical researchers from with making the practice of genomics mantheir primary focus, the patient. ageable in recent years. There is no question that the explosion of heretofore inaccesBy concentrating on the approximately 400 genes that the resible data on the nature of disease, generated by genomics and search community is most familiar with—genes associated with channeled through bioinformatics, has moved the ball forward the mutations in more than 2% of patients with particular canin drug research. Access to reams of new data has also moved the cers—screening becomes a far less haphazard enterprise than takgame onto a new field, one that reveals the heterogeneous nature ing on an entire genome of 25,000 genes. And with the increased of disease. Genomic information has become the key to identifyfocus on relevant genes comes a feasible means of substituting a ing patients who will respond to therapies that would not come manageable screening set of hundreds of genes for a single, possianywhere near the clinic in a blockbuster drug development bly misleading, biomarker in clinical trials. mode. The annual Bio-IT World conference, which took place in Boston GENOMICS HAS REACHED a tipping point, Rothberg insists. “It’s last month, provided an excellent window on the benefits as well as the opposite of what genomics has been for the last 20 years.” Rethe distractions of the current data storm in pharmaceutical labs. searchers are no longer gathering overwhelming quantities of data. The preponderance of data in drug research was made palpable with “Now, they are working with panels of 200 to 400 cancer genes, three days of 12 parallel sessions bearing titles like “An Algorithm knowing exactly what these genes do.” And the work is being done for Identifying Multiply Modified Endogenous Proteins Using Both in the clinic. “I have never seen so much focus on translational use Full-Scan & High-Resolution Tandem Mass Spectrometric Data.” of sequencing as I have in the last six months,” Rothberg says. Then, at a day-three panel discussion on challenges in cancer reThe fact that Harvard is now contemplating a formal cursearch, there came a moment of epiphany. Julian Adams, president riculum for bioinformatics may be further indication that some of Infinity Pharmaceuticals; John Quackenbush, a bioinformaticist kind of clarity is emerging from the data chaos. Bioinformatics is at Dana-Farber Cancer Institute and Harvard School of Public becoming a discipline that will deliver tools and information to Health; and other panelists seemed to raise the collective call: “It’s researchers “in ways that make sense,” Quackenbush said at the the patient, stupid!” Bio-IT World panel discussion. Ideally, data will be presented in The panelists discussed new approaches to making sense of the a format that allows clinicians to edit rather than analyze genetic data generated in genomics-based drug discovery and developcontent, he said. ment that have less to do with computers than with Quackenbush went on to affirm the crucial second patients in clinics. The group envisioned a kind of virtustep in the genius process:“And we need to communicate ous circle in which data are put to the task of identifying the mission of what you’re doing back to the public.” patients most likely to respond to therapies, and trials “For a lot of Back, that is, to the patient. people, data are designed to vet the data coming in, eliminating the extraneous and creating knowledge applicable to do become a Views expressed on this page are those of the author clinical trials. and not necessarily those of ACS. distraction.” SHU T T ERSTO CK
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