MIAMI BEACH, Fla.--Attendees and exhibitors at the Tenth International Genome Sequencing and Analysis Conference (GSAC), held here September 17-20, said that despite the fact that the tone of the meeting has changed because of expanded attendance, increasing commercial influence, and recent developments that have stirred competitive fires among human genome sequencing efforts, the event was a success. The annual conference is sponsored by the Institute for Genomic Research (TIGR).
More than 80 exhibiting companies and some 1,800 attendees gathered here for three days and two nights of speeches, plenary sessions, paper and electronic poster presentations, and product exhibits representing the latest technology and practices in genomic sequencing. The meeting was brought to an extravagant close with a 10-year anniversary bash Sunday night hosted by TIGR and Celera.
The newly accelerated race to sequence the human genome was a strong undercurrent at GSAC: announcements in recent months by TIGR founder Craig Venter, who teamed up with Perkin-Elmer to create Celera, a new company that will sequence the human genome within three years, and Incyte Pharmaceuticals, which launched its own effort to map the human genome within one year, have sent shockwaves through the genomics community. Just three days before GSAC commenced, the federal Human Genome Project created another stir by revising a five-year plan in order to finish its project two years ahead of schedule.
Gene Myers and Mark Adams, new recruits to Celera, addressed those skeptical of their company's chance to achieve its goals in speeches on whole-genome shotgun sequencing. "Myers's talk gave me a better sense of what they are trying to do from a computational standpoint, but theory and reality do not always intersect," commented an attendee who remained skeptical.
Susan Strong, vice-president for software company Genomica, said that, as a vendor of bioinformatics tools, she's invigorated by the competitive developments that will "create a lot of data that need to be managed by products like ours."
Others expressed concerns that, because of TIGR's new ties to the commercial world, future GSAC conferences may not be as impartial as those in the past. One attendee claimed to notice "a significant bias towards TIGR, Celera, and Perkin-Elmer speakers and chairs," which he called "unfortunate and damaging to credibility in a scientific show of this caliber."
Attendees noted several particularly interesting speakers. "The high spot of the conference was the presentation by George Poste from SmithKline Beecham," commented Steve Gardner, CEO of the UK firm Synomics. "He presented a vision of the significance of genomics and related developments to the pharma, biotech, and agro industries, combined with detailed examples of the profound impact that these will have on individuals, groups, and society at large. The only downside was that he was limited to half an hour. I would have been happy to listen for a couple of hours."
A series of presentations Friday evening defined the importance of genomics to agriculture. Ganesh Kishore of Monsanto, Steve Tanksley from Cornell, and Harvard business professor Ray Goldberg addressed the future role for genomics in providing for human nutrition and animal feed supplies.
An address by Glaxo Wellcome's Allen Roses on the acceleration of pharmacogenetics impressed upon listeners the potential in this new area. Bayer's worldwide coordinator of bioinformatics, Douglas Bigwood, observed, "This area will be the prime focus for the pharma industry for many years to come. Bioinformatics will play a key role in this area due to that fact that polymorphisms in humans create very complex and diverse metabolic interactions." He continued, "It will be a case where software development will necessarily go hand-in-hand with drug development."
Stanford's David Cox showed, as one listener put it, "why he is one of best thinkers in the area of mapping and sequencing and that he is also very much a pragmatist." Cox presented a case for placing "BAC's on the map" rather than the other way round, and explained why a map of48,000 STS's is insufficient.
TECHNOLOGY EVOLUTION, NO LONGER REVOLUTION
Several attendees expressed disappointment over a shortage of exciting bioinformatics developments shown at GSAC. "It's not that presentations were poor," remarked Bigwood, "but it was just more of the same with improvements in speed and interfaces. Perhaps that's a sign that bioinformatics is maturing and that advances will be evolutionary instead of revolutionary," he added.
And while some also criticized a lack of thrilling new technology on the exhibit floor, others found plenty there to talk about.
"The most remarkable to me was the presence of at least four companies with capillary sequencing instruments," said Todd Smith, president of bioinformatics company Geospiza. "Capillary technology is becoming robust and is now reduced to practice. We are at the beginning of the same type of performance/cost curve that computers have gone through," he observed.
Smith also noted significant progress in hybridization chips, but remarked that the bottleneck that prevents effective use of these technologies is in informatics.
Synomics's Gardner said his interest was piqued by a few software vendors: "SeqStore and Omiga 1.1 from Oxford Molecular marked an important return to fortune for Oxford Molecular and Genetics Computer Group," Gardner said. "Spotfire and Neomorphic also had interesting displays," he added. Gardner was also pleased with the attention his own company, a startup, received from end-users and vendors for its recent collaboration with Incyte.
Exhibitors who spoke with BioInform, most of whom were flooded with traffic morning-to-evening, were generally satisfied with the turnout. Paracel's Marty Leventhal summed up many vendors' sentiments this way: "This conference dwarfs all others in both attendance and value."
The following companies were among those demonstrating bioinformatics products at GSAC:
Affymetrix http://www.affymetrix.com launched several bioinformatics tools and an extended portfolio of GeneChip gene expression monitoring products that include high-density oligonucleotide arrays that can simultaneously analyze gene expression levels of approximately 30,000 mouse genes and expressed sequence tags (EST's), and over 40,000 human genes and EST's. Affymetrix's new GeneChip Laboratory Information Management System enables customers to track processes, data, and samples across experiments and is compatible with GeneChip 3.1 software as well as all Genetic Analysis Technology Consortium-compatible genetic information management systems. The GeneChip Expression Data Mining Tool allows scientists to sift quickly through expression data using custom queries.
Amersham Pharmacia Biotech http://www.apbiotech.com demonstrated the MegaBACE 1000, a high-throughput capillary system for DNA sequencing. The system was recently installed at the world's largest public sequencing center, the UK's Sanger Centre. It was developed jointly by Amersham and its new wholly owned subsidiary,
Molecular Dynamics http://www.moldyn.com. Before the conference Molecular Dynamics announced a collaboration with Beckman Coulter http://www.beckmancoulter.com to develop a robotic system to integrate and automate the operation of multiple MegaBACE units, allowing linking of up to four of the instruments to enable the unattended processing of 4,600 samples and sequencing of more than 2 million bases in a 24-hour period. Molecular Dynamics also announced a collaboration with Cimarron Software http://www.cimsoft.com to integrate the MegaBACE platform into Cimarron's laboratory information management system. The Cimarron LIMS will be offered as part of the MegaBACE package for high-throughput operations.
ApoCom http://www.apocom.com introduced GeneHound, a tool for identifying coding regions within DNA that uses an algorithm based on measuring correlations between nucleotides in specific codon positions and those in neighboring codons. Used to predict genes, GeneHound compares observed correlations to those predicted by the model. GeneHound calculates the statistical significance of the relationship between observed and expected genes to be used as the discrimination function for gene detection. Start and stop positions of the coding region are determined by observing the rate of change of this function and searching for start and stop codons where the absolute magnitude of the function is highest.
Geospiza http://www.geospiza.com demonstrated its Finch Chromatogram Server in an electronic poster. The server automates quality assurance procedures and applies statistical process control to reduce the cost of high-throughput DNA sequencing. The chromatogram server encapsulates the phred base-calling algorithm to analyze sequence length and quality in real time, and monitors system performance to address issues encountered when planning for higher capacity. A web-based interface is used to control applications, enter information, and view system reports.
National Center for Genomic Resources http://www.ncgr.org demonstrated tools for retrieving and analyzing data stored in its Genome Sequence Database, including the beta version of Sequence Viewer, a tool for dynamic retrieval and navigation of graphical representations of nucleotide sequences in the database. Available as a Java applet or application, Sequence Viewer also allows users to obtain detailed text descriptions of the annotated characteristics of sequences.
Neomorphic http://www.neomorphic.com exhibited the Labtrack system for managing the DNA sequence production pipeline, and a suite of genomic data visualization and analysis software products. The Neomorphic Genome Software Development Kit, created in collaboration with Berkeley's Drosophila Genome Project, allows customers to build applications by integrating widgets, including a viewer for physical or genetic maps; an assembly viewer; a histogram of base-calling quality scores; a sequence residues viewer; and a sequence trace viewer. Scrolling and semantic zooming are built in, and drill down and linkage is provided between products.
Netgenics http://www.netgenics.com demonstrated its Synergy product, which integrates diverse analytical tools and data, and allows research team members to share them from a common user interface. The product includes software, hardware, and development services and support.
Pangea Systems http://www.pangeasystems.com demonstrated GeneWorld 3.0, the latest version of its automated, high-throughput software application for sequence analysis and decision support. The product includes features to speed the transformation of bioinformatics data into useful knowledge and to help researchers make rapid, informed decisions to accelerate drug target discovery.
Paracel http://www.paracel.com demonstrated for the first time GeneMatcher, a new parallel processor for sequence analysis. GeneMatcher, containing 6,912 ASIC processors, combines the power of a supercomputer into an open-systems network server. It accelerates dynamic programming algorithms such as Smith Waterman, hidden Markov models, and other computationally intensive genomic searches.
Silicon Graphics http://www.sgi.com/chembio demonstrated workstation and server technologies including O2 and Octane desktop systems, Origin servers, and Cray supercomputers. The company showed MineSet, a datamining and visualization toolkit, and the SGI technology used to support 3D Crunch, a large-scale comparative protein modeling computation of Swiss-Prot sequences.
Spotfire http://www.spotfire.com exhibited Spotfire Pro 3, the third generation of its database discovery and exploration product. Spotfire Pro is used to support early-stage research activities in high-throughput screening, genomics, lead optimization, combinatorial chemistry, chemical formulation, and biostatistics. The product displays large amounts of disparate data and allows visual queries of the information for trends, anomalies, outliers, and patterns. Users can generate reports, web pages, annotations, and interactive analysis files that can be distributed via e-mail and the internet. The Spotfire Pro Windows 3.11/95/NT demo version allows exploration of a range of datasets provided with the demo with all the functionality of full Spotfire Pro.
In addition, the following exhibitors' new products were included in preconference coverage in the September 14 BioInform: Base4 Bioinformatics http://www.basefour.com; Compugen http://www.cgen.com; Genetics Computer Group http://www.gcg.com; Oxford Molecular http://www.oxmol.com; and Time Logic http://www.timelogic.com.