Created: 3rd January 1999, last updated: 4th January 1999, © 1999 ABRF
Paul Morrison
Dana-Farber Cancer Institute, Boston, MA
The 10th International Genome Sequencing and Analysis Conference has been held in Hilton Head, South Carolina for the last eight years. Due to skyrocketing attendance, the tenth conference was held at the Fontainebleau Hotel in Miami, Florida on September 17-20, 1998. Of concern to long time attendees was whether the small meeting atmosphere could be retained after moving to the larger venue in Miami. As it turned out, these concerns were unwarranted, even with attendance reaching 1900 people.
An ABRF sponsored roundtable discussion was held at the conference for the second year. This well-attended session was titled "Getting it Right: Current Technology and Methodology in DNA Sequencing Core Facilities." The session was chaired by Duane Bartley, Johns Hopkins University, who described the ABRF, its mission, and membership benefits. Scottie Adams, Trudeau Institute, outlined the results of the DNA Sequence Research Group's recent study, which included 242 sequencing runs collected from 72 different machines in 59 participating facilities. George Grills, Albert Einstein College of Medicine, described the results of experiments aimed at optimizing DNA sequencing quality and throughput, including modifications that enable practical implementation of the 96 lane upgrade on the ABI 377 sequencer and the results of using different types of porous combs to facilitate the loading of large numbers of samples. Greg Buck, Virginia Commonwealth University, presented the Nucleic Acids Research Group's study on "DNA Sequencing Primer Design Strategies and Performance." As happened last year, a lively discussion with the audience followed these presentations, with representatives of reagents and instruments joining in the fray.
In addition to organizing the roundtable discussion session, The ABRF DNA Sequencing Research Group presented the details of the results of its latest study in a poster session at the conference. The poster was titled "Analysis of the Effects of Different DNA Sequencing Methods on Sequencing Quality, Creation of a Quality Control Resource, and Assessment of the Current State of the Art" (Grills G., Adams PS, Dolejsi MK, Hardin S, McMinimy D, Morrison P, Rush J, and Thannhauser T. (1998), Microbial and Comparative Genomics 3(3), C-88). The poster presentation generated a lot of interest and discussion, both about the specific results of the study and the general role of the ABRF.
A deluge of different poster sessions and vendor exhibits every day of the meeting showcased an incredible array of different ways to sequence DNA. The consensus one might conclude is that there is no "right way." Each laboratory does sequencing differently to best match the type of project that is being performed.
There were a number of questions on the mind of ABRF members from core sequencing laboratories who were attending the meeting. Is there going to be any sequencing left after these genomes are done? What new technologies can be incorporated into core sequencing laboratories in the near future?
Several plenary sessions answered the first question affirmatively. Single nucleotide polymorphisms (SNPs) were the main topic of the first plenary session. Each one of us carries these single base changes that, if known, could be used as a bar code to distinguish our genetic fingerprint from everyone else. For instance, these polymorphisms could identify individuals predisposed to adverse drug reactions. In addition, specific therapeutic agents could be designed for carriers of certain patterns of SNPs. The social implications of these potential applications were discussed, as individuals with undesirable SNPs may have difficulty obtaining health care and a desirable SNP pattern could ultimately define the top tier of a new class structure.
Other plenary sessions described projects connected with the completed, or soon to be completed, genomes. Gerald Rubin described the mutation of every Drosophila gene in order to characterize the function of each reading frame. It seems apparent now that once the last nucleotide of each genome is finished the sequencing and informatics has just begun.
Of interest to ABRF mass spectrometrists was a talk by John Yates in which he described the use of microcolumn liquid chromatography interfaced to a tandem mass spectrometer. He showed results of deconvoluting data from large protein complexes and total cellular proteins.
Microarrays made a big showing at the conference. Microarray technologies, applications and results were presented in plenary sessions, posters, and exhibits. Many presentations included products that are now being shipped. Attendance at George Grills' session on "Implementing Microarray Technologies in Facility Laboratories" at the March 1999 ABRF meeting will be mandatory for understanding how these new instruments can be applied and how they can be successfully incorporated into a shared-use facility.
Last, but certainly not least, the conference featured presentations from the Celera Genomics Corporation (CGC), which is the name of the Craig Venter and Mike Hunkapiller venture that is promising to sequence the human genome in 3 years for only 300 million dollars. The PE Applied Biosystems 3700 capillary-based DNA sequencer that is to be the workhorse for this enterprise was unveiled and put on display. The 3700 is a fluorescence-based DNA sequencing system utilizing capillary electrophoresis with 96 capillaries operating in parallel, giving an amazingly high throughput potential. The latest version of the Amersham/Molecular Dynamics' MegaBace 1000 capillary-based sequencer and many other new sequencing technologies were presented as well. It is too early to tell when one of these instruments will find a home in a resource laboratory. The 3700 is not shipping yet. The read lengths of this and many of the other new types of instruments are not up to what is typically being achieved in core labs. If one can accept shorter read lengths, a major question will be how to modify procedures so that a ten-fold increase in templates can be accepted and processed. On the front end, robotics seem to be a necessary part of sample handling. On the back end, the processing of data has to be streamlined to accommodate the huge increase in information.
The meeting ended with a lavish dinner at the Villa Vizcaya Museum, sponsored by CGC, with Bruce Hornsby as the musical entertainment. Let's hope this will also become a time-honored tradition.
This summary only scratches the surface of this very methods-intensive conference. The program and abstracts listing speakers and poster presenters for the 10th International Genome Sequencing and Analysis Conference are published in Microbial and Comparative Genomics, Vol. 3, No. 3, 1998. This journal is now indexed by Medline, so it is possible to search for specific authors or methods on-line. The date and agenda of the 1999 meeting will be posted at www.tigr.org.