created: 14th January 1998, last updated: 14th January 1998, © 1998 ABRF
The Ninth International Genome Sequencing and Analysis Conference sponsored by TIGR (The Institute for Genomic Research) was held September 13-16, 1997 on Hilton Head Island, SC.
The cooperative international effort to sequence and analyze the genomes and proteomes of humans, microbes, plants and other organisms marches onward. The highlights of this year's conference focused on the crucial issues of speed and cost; the development of novel methodologies, instrumentation, and bioinformatics strategies to make the sequence generation and annotation process faster and cheaper.
Plenary Sessions were held on Microbial Genomes, Microarrays, Functional Analysis, Eukaryotic Genomes, Genome Biology, Advanced Technology and New Approaches, and the Human Genome. Break-out sessions concentrated on Bioinformatics, Technology, and Genomics. Sequencing project updates, technological innovations, and sequence strategies on the Human Genome project were presented by representatives from TIGR and Genome Sequencing Centers at Washington University, Baylor College of Medicine, University of Texas Southwestern, University of Oklahoma, University of Tokyo, The Sanger Centre at Cambridge, UK, University of Washington, the Stanford Human Genome Center, Institute of Molecular Biology in Jena, Germany, and the Rice Genome Research Program in Tsukuba, Japan.
Among the highlights of the meeting:
* Mark Adams, from TIGR, described the latest advances in bacterial artificial chromosome (BAC) end sequencing and their collaboration with the California Institute of Technology in sequencing the short arm of human chromosome 16. Annotater, a Java program that displays database matches to both proteins and expressed sequence tags (ESTs) to supplement gene prediction programs such as GRAIL and GENEFINDER, was described.
* The Genome Sequencing Center at Washington University, where more than 30 Mb of human chromosome 7 have been sequenced, reported on techniques for expanding lane density of PE/ABD DNA sequencers to 96 lanes.
* The Chromosome 11 project at the University of Texas Southwestern has spawned such innovations as the MERMADE, a high throughput automated oligonucleotide synthesizer, and the software Primo which takes assembly data from the programs Phred and Phrap and feeds instructions directly to MERMADE.
* Bruce Roe, University of Oklahoma reported on the comparison of human chromosome 22 with syngeneic regions in the mouse genome. It was observed that exon spacing is well conserved from mouse to human but intron spacing is very different.
* Yoshiyaki Sakaki, and his colleagues from the University of Tokyo Human Genome Center, have identified 61 genes on chromosome 21, seven of which are believed to be critical for Down's syndrome.
* Strategies for constructing third generation maps of the human genome using DNA microarrays to detect single base polymorphisms were presented by Eric Lander, of the Whitehead Institute at MIT.
* Lee Hood, University of Washington, discussed the duplication or deletion of long sequence repeats as an evolutionary strategy for controlling the size of complex gene families such as the T-cell receptor loci.
* A consortium of 134 European laboratories, EUROFAN, is pursuing the proteome analysis of the completed yeast genome to identify the function of more that 2000 ORF's that have no homology to known genes and to generate deletion strains and cassettes for all S. cerevisiae genes.
* Scientists at Lawrence Berkeley National Laboratory have sequenced 7.8 Mb of the Drosophila genome and are progressing at the rate of 7Mb/year. This group is collaborating with Motorola to assess the benefits of applying modern manufacturing principles to the sequencing process.
* Nearly one fifth of the Arabidopsis genome is completed. Of the 20,000 genes identified, many are repeated, only 15,000 are unique. It is speculated that gene duplication and recombination is an evolutionary strategy to achieve disease resistance specificity.
* Nearly 71% of the 100 Mb C. elegans genome is complete. 43% of the predicted proteins are similar to non-worm proteins. Of the 84 human disease genes that have been identified by positional cloning, 54 have homologues in the C. elegans genome. A structural finding of interest is that some genes lie within introns of other genes on the opposite DNA strand.
* In microbial systems, a Japanese and European consortium has sequenced the 4.2-Mb genome of Bacillus subtilis. Progress was reported on the sequence and analysis of the genomes of Mycobacterium tuberculosis, Treponema pallidum, Borrelia burgdorferi (Lyme disease), and a strain of E. coli responsible for recent food poisoning outbreaks. A comparative analysis of Rickettsia prowazekii and Reclinomonas americana has provided insight into the origin of mitochondria.
* Microarray technology for massive parallel expression analysis was the focus of one of the plenary sessions with presentations from Affymetrix, Stanford University, Rosetta Biosystems, and Molecular Dynamics.
* Perkin-Elmer/Applied Biosystems Division (PE/ABD) introduced their new ABI Prism BigDye terminators which are single molecule energy transfer primers containing dichlororhodamine dyes as acceptors. These dyes yield less spectral overlap, reduced background noise, more even peak height, and low mobility shifts. The BigDyes are similar to the recently introduced dichlororhodamine (dRhodamine) dyes but have been coupled to a second dye resulting in increased sensitivity. Direct sequencing of BACS is said to be greatly improved. The major drawback to these new dyes at this time, is that they can only be used on the newest Model 377 DNA sequencer, leaving thousands of 373 owners unable to take advantage of the new technology.
A new feature of the conference this year was an ABRF-sponsored roundtable presentation organized by the Education Committee and the DNA Sequence and Nucleic Acids Research Groups. The 2 1/2 hour session was titled "Current Methodologies Used in DNA Sequencing Core Laboratories" - subtitled "The Agony and the Occasional Ecstacy". The session was chaired by Duane Bartley, Johns Hopkins University, who briefly described the ABRF, its mission, membership benefits, and the function of its research committees. Presentations were made by Pamela Scott Adams, W. Alton Jones Cell Science Center, describing the DNA Sequence Research Committee's recent study on the "Effects of DMSO, Thermocycling and Manual Editing on DNA Sequence Accuracy of a 72% GC Rich Template". Greg Buck, Virginia Commonwealth University, presented the Nucleic Acids Research Group study on "DNA Sequencing Primer Design Strategies and Performance". Susan Hardin, University of Houston, discussed "Octamer Primed Cycle Sequencing Using Fluorescent Chemistry". The latest problems in DNA sequencing technology brought about by the introduction of the PE/ABD XL upgrade and the dRhodamine dyes were discussed by George Grills, Albert Einstein College of Medicine, and Margaret Robertson, University of Utah.
Refreshments were generously provided by Perkin-Elmer/ Applied Biosystems Division. Many representatives of PE/ABD were present to participate in the lively discussions that followed, including Shiaw-min Chen, developer of the new dRhodamine and BigDyes. The session was planned in anticipation of 50 participants but there was 2-3 times that number present, creating a standing room only environment. Positive feedback was abundant and almost all ABRF recruiting material was picked up by interested participants. Conference organizers were enthusiastic about making the ABRF session an annual part of the conference.
Three poster sessions including numerous electronic posters and fifty-four exhibitors introduced the latest in technology in the DNA sequencing world.
The program and abstracts listing speakers and poster presenters for the Ninth International Genome Sequencing and Analysis Conference are published in Microbial and Comparative Genomics, Volume 2, Number 3, 1997.
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