Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News, March 1993; 4(6)
GENOME CENTER:
Lawrence Berkeley Laboratory
(DOE; established 1988)
DIRECTORS:
Jasper Rine
Sylvia Spengler, Deputy Director
CONTACTS:
Sylvia Spengler
(510/486-4879, Fax: -5717; sylviaj@ux5.lbl.gov)
Jasper Rine (-4047; jdrine@lbl.gov)
Lawrence Berkeley Laboratory
Human Genome Center
459 Donner Laboratory
1 Cyclotron Road
Berkeley, CA 94720
OTHER KEY RESEARCHERS:
Jan-Fang Cheng, Jeff Gingrich, Joseph Jaklevic, Christopher Martin, Victor Markowitz, John McCarthy, Elaine Ostrander, Michael Palazzolo, Stewart Scherer, Ed Theil, Manfred Zorn
MAJOR GOALS:
- Assembly of physical maps of complete chromosome arms rooted in templates appropriate for sequencing, and development of the capacity to produce genomic sequence of multiple megabases per year. One target is the long arm of chromosome 21.
- Development of automation and informatics neceary to produce an effective sequencing assembly line and capture, assemble, analyze, and distribute massive amounts of sequence information.
MAJOR ACCOMPLISHMENTS:
- Completion of an 80-kb P1 clone sequence in 4 months, building on a high-resolution physical-mapping strategy (DOG-tagging) that generates distance, orientation, and gene size resolution (3 kb).
- Development of novel mapping resources for chromosome 21, including 49 mapped cDNA clones, over 40 dinucleotide repeat-based genetic markers, a YAC contig map, a set of somatic cell radiation hybrids [with David Cox (Stanford Univ.)], a cytogenetic map of the long arm enriched by FISH with 280 YACs and cosmids, and 188 clones forming 21 multiple YAC contigs and 4 single YAC contigs.
- Development of several instruments supporting automated mapping and sequencing, including a 96-sample thermal cycler for PCR, an imaging station for mapping and sequencing procedures, gel fractionations of PCR products, and an automated colony picker.
- Development of companion software, including HGCdb, a database variant of ACEDB; a sequence analysis package; database management tools, including ERDRAW, SDT, QST, and OPM Editor; and an automated generator of a user interface that responds to changes in an underlying database.
AVAILABLE RESOURCES:
- Automated colony picker and imaging station with supporting hardware for gel casting (Martin Pollard, 510/486-4561).
- Database management tools: ERDRAW, a graphical editor for entity-relationship schemes; SDT, a translator of relationships; OPM Editor, a graphical editor for object-protocol schemes; and QST for specification of queries (Markowitz, vmmarkowitz@lbl.gov).
- Sequencing-analysis software available for testing; improved interface being developed (stew@genome.lbl.gov).
- Biological resources: polymorphic genetic marker clones (Ostrander, 510/486-6946); mapped YACs and P1 clones on 21 (Gingrich, -6580); and mapped cDNA clones on 21 (Cheng, -6590).
Genome Centers Acronym List
HGMIS Staff
Return to List of Genome Centers
Return to Table of Contents
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v4n6).
