Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Human DNA Sequencing at the LBL Human Genome Center

Michael Palazzolo, Christopher Martin, William Kimmerly, Edward Rubin, J. F. Cheng, Joseph Jaklevic, Edward Theil, and Mohan Narla.
Human Genome Center, Lawrence Berkeley Laboratory, University of California, Berkeley, CA 94720

The Human Genome Center (HGC) of the Lawrence Berkeley Laboratory is oriented almost exclusively towards developing and implementing directed methodologies for cost-effective and accurate high throughput human DNA sequencing. This work has five components. The first three components of the Center are all involved with new technology development for sequencing and are based on a collaboration between biologists, the automation group, and computer scientists. The fourth component is the sequencing production effort itself. The fifth component of the HGC is the biology effort that interfaces and performs experiments derived from the completed sequence data. The biology component of the new technology group has developed a directed strategy of DNA sequencing in which high resolution physical maps are generated so that a small set of standard primer binding sites are positioned every 300 bp. This mapped set of templates is then sequenced. Using this strategy templates can be selected in a minimally redundant fashion which means that template preparation requirements are reduced tenfold and sequencing reactions can be reduced five-fold. In addition, sequence assembly is straightforward because all the templates are mapped in relation to each other, with a resolution of about 30 bp, prior to sequencing. The biology group is continuing to optimize the biological procedures of the directed process. The second component of the center is the work of the automation group which is developing instrumentation to support the directed sequencing approach. Some of the modules have been completed and are currently in use: an image station that captures and analyzes the mapping information from agarose gels, a colony picker, a robotic library replicator, and a modified Biomek that sets up PCR assays and sequencing reactions. A water-based thermocycler and a 12-channel oligonucleotide synthesizer are being rigorously tested by the biologists prior to entering production. Novel methods to analyze PCR fragments as well as preliminary plans to integrate some of the initial modules are in the early planning stages. The third component of the HGC is the informatics group. The major goal of the group is to develop software that facilitates the sequencing effort. The developmental effort is aimed at all aspects of the process, beginning with the physical mapping efforts, continuing through the generation of the high resolution map and template selection, followed by sequencing and assembly of templates and concludes with the analysis and dissemination of the sequencing information. The programs that keep track of and display the physical mapping data are nearing completion. The emphasis of the work is shifting now to sequence assembly, editing, and analysis. Another aspect of the work is focused on developing mechanisms to make the data publicly accessible as it is being generated. The fourth component of the center is the production effort. A team of 5-6 FTE's can currently generate 600-700 kb per year. The goal of the production effort is to maintain this rate as well as to add additional teams in the next few years and also increase the productivity of each team. The final component of the HGC is the biology program which has been reconstituted to be closely integrated with the overall sequencing effort. The biology effort will play a role in selecting templates beforehand and then developing biological approaches to interpret such a large amount of data in a meaningful way.