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.

Directed Genomic DNA Sequencing

Christopher H. Martin, Cheryl A. Davis, Carol A. Mayeda, Herb Moise and Michael J. Palazzolo
Human Genome Center, Lawrence Berkeley Laboratory, Berkeley, CA 94720

Our group has developed a novel directed approach to genomic sequencing in which every sequencing template is mapped to a resolution of 30 base pairs prior to being sequenced. This high resolution mapping information yields two important advantages. First, genomic sequence can be determined with far fewer sequencing reactions than approaches which utilize random coverage to obtain the bulk of the complete sequence. Second, the difficulty of the sequence assembly problem is greatly reduced, as the mapping information provides significant assistance to the reconstruction of the original sequence.

This project is supported by a unique collaborative arrangement between NIH and DOE. The Department of Energy is funding organism-independent technology development for the directed sequencing strategy, and also production genomic DNA sequencing in humans. NIH is funding Drosophila production sequencing.

Our group has sequenced over 1,500,000 base pairs of human and Drosophila genomic DNA using the directed sequencing approach. We currently have two 6.5 member sequencing teams in operation. The first is DOE funded and is focusing on a 1.2 Mb growth factor cluster surrounding the interleukin-4 gene on human chromosome 5. The second team is NIH funded and is targeted at a genetically well characterized region of approximately 2.2 megabases that surrounds the Adh gene of Drosophila.

Our goal is to use the directed sequencing strategy as a biological platform for the collaborative development of a highly automated system for the sequencing of genomic DNA. We work in close collaboration with the automation and computation groups of the Human Genome Center at LBL in order to pursue this goal of reducing the labor requirement of genomic sequencing. The ability to develop custom hardware and software modules that address the scope of the genomic sequencing production work is essential in our efforts to reduce the cost of genomic sequencing. Several of these automation and informatics modules are already in routine production use and are having a major impact on the efficiency of the directed sequencing process. The functioning of some of these modules in a production sequencing environment and their effect on productivity will be presented. Several additional modules are now being tested or are under construction and are aimed at further increases on the throughput of the process.

The two production teams (one is dedicated to Drosophila sequencing, the other to human sequencing) of the Directed Sequencing Group consist of Marnel Bondoc, Annie Chiang, Thomas Clouder, Paul Critz, Cheryl Davis, Cheryl Ericsson, Michael Jaklevic, Robert Kim, Michelle Lee, Melvin Li, Carol Mayeda, Afaf Steiert-El Kheir and Millicent Yee.