Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News, March 1993; 4(6)
(NIH; established 1990)
Glen A. Evans
Harold H. Garner, Associate Director
Michael W. Smith, Assistant Director
Glen Evans (619/453-4100, x 279, x376 (lab), Fax: /558-9513 or firstname.lastname@example.org)
Suzanne Clancy (Center Administrator, x 340 or x151)
The Salk Institute
P.O. Box 85800
San Diego, CA 92138
Harold H. Garner (619/455-3464, Fax: -2464; email@example.com)
General Atomics Corporation
P.O. Box 85608
San Diego, CA 92186
OTHER KEY RESEARCHERS:
Stephen Clark, Karin Diggle, Jane Hutchinson, Lisa Leonard, Ying Lin, David McElligott, John Quackenbush, Tony Romo, Licia Selleri, Ken Snider, Yalin Wei
General Atomics: Barbara Armstrong, Whitney Cunha, Dan Kramarsky, Mary Petrowski
- Assembly of a human chromosome 11 STS-content map with resolution of <500 kb and a low-resolution yac contig map of nonchimeric yac clones.
- Assembly of a high-resolution "sequence-ready" cosmid contig map of human chromosome 11 and other chromosomes, using manual and automated approaches.
- Construction of high-resolution sequence-sampled maps of several human chromosomes, consisting of 30 to 60% of the DNA sequence in one pass and analysis of the sequence for content.
- Development of technology, strategies, and instrumentation for large-scale, high-throughput, automated high-resolution physical mapping.
- Development of an integrated system using an entirely automated approach for sustained high-throughput, one-pass DNA sequencing at a rate of 60 Mb/year and $0.03/bp.
- Development of informatics and computational tools using parallel processing computers for analysis of genomic DNA sequence.
- Production of resources necessary for rapid identification and isolation of disease genes.
- Completion of 300-kb resolution STS map of chromosome 11 based on cosmid end sequencing and containing STS identifiers for all known genes; construction of a low-resolution chromosome 11 physical map with 90% coverage in nonchimeric YAC contigs; 150 cosmids and > 200 YACs mapped by FISH. Current chromosome 11 map contains over 2000 loci.
- DNA sequence determined for 0.3% of chromosome 11.
- Development of technology for high-throughput automated DNA sequencing (using cosmid templates) and template preparation ("Dr. Prepper" robotics system), high-volume sample handling (GAS robotics), parallel processing sequence analysis (GIST), automated high-throughput PCR, and automated arrayed library analysis.
- Identification of a leukemia-associated transcription factor gene (HTRX) responsible for > 80% of infant leukemias and representing the human homologue of the Drosophila trithorax (trx) gene.
- Development of high-density plasticware in 384 thin-walled, 384, and 864 well formats and accompanying tools for the Beckman Biomek.
- Development of Genome Notebook, a portable, network-accessible relational database for genome mapping and sequencing data.
- Cosmid libraries: Arrayed chromosome 11-specific cosmid libraries - SRL, 16,000 clones; 11q (11q13-11qter), 1200 clones. Arrayed cosmid libraries for chromosomes 5 and 16. Giardia cosmid libraries (12,000 clones, 2 hosts) and chromosome-specific subsets (Smith).
- YAC libraries: Total genome - St. Louis; CEPH Mark I; CEPH Mark VI to VII (megabase). Chromosome 11-specific (T. Shows, RPMI, Buffalo, NY). Chromosome 21 minimal tiling set.
- STSs: Over 390 STSs produced by this lab and > 1000 STSs for chromosome 11 (available online via Salk Internet GOPHER server).
- Cell hybrids: 15 cell hybrid chromosome 11 mapping panels; monochromosomal hybrids for all human chromosomes.
- Instrumentation: "Dr. Prepper," GAS, GIST, PCR system, Hyb system (Garner).
- Robotics for Biomek and plasticware (Helix,, Inc.).
- Autopooling system (Evans or Quackenbush).
- Genome Notebook [Macintosh demo disk (Clark)].
Genome Centers Acronym List
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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).