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Human Genome News Archive Edition

Human Genome News, March 1993; 4(6)

GENOME CENTER:

Salk Institute

(NIH; established 1990)

DIRECTORS:
Glen A. Evans
Harold H. Garner, Associate Director
Michael W. Smith, Assistant Director

CONTACTS:
Glen Evans (619/453-4100, x 279, x376 (lab), Fax: /558-9513 or gevans@salk-sc2.sdsc.edu)
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; garner@vaxd.gat.com)
General Atomics Corporation
Biosciences Division
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

MAJOR GOALS:

  • 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.

MAJOR ACCOMPLISHMENTS:

  • 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.

AVAILABLE RESOURCES:

  • 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)].

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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).

Human Genome Project 1990–2003

The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.