Progress, and Applications
of the Human Genome Project
Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
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In this issue...
DOE '99 Oakland Highlights
In the News
Web, Other Resources, Publications
Sequencing at Other Institutions
New Strategies, Resources Reported
Report from 1999 DOE Genome Meeting
The exciting potential of high-throughput sequencing was evident as presenters detailed progress in effective strategies for handling repeat telomeric regions, high-speed DNA analysis systems, and new vectors.
Verifying Sequence of Subtelomeric Regions
This technology allows restriction maps to be constructed directly from genomic DNA rather than from DNA clones that are more prone to rearrangements. Using DNA from PCR products generated on genomic DNA, the UC researchers also resequenced about 18% of the 0.13-Mb 7q telomere. These methods confirmed prior mapping and sequencing results. The group is completing the mapping and sequencing of two additional telomeres, 9q and 11q, and next will target telomeric regions of chromosomes 5, 16, and 19.
BAC Update: New Vectors, Sequencing Progress
At the Oakland meeting, Melvin Simon (California Institute of Technology) talked about new BAC vectors for the genome project and for tagging BAC clones with gene information to enhance research into gene function in animals and plants. The number of human BAC clones generated is now close to one million. Simon's team has been annotating the "D" library [used for BAC-end sequencing at The Institute for Genomic Research (TIGR) and the University of Washington (UW, see "Gene Riches of Chromosome 19 Revealed")] with ESTs obtained from I.M.A.G.E. Consortium resources.
Simon also reported the development of a new BAC vector and an improved method of constructing BAC libraries. The group has begun constructing a series of BAC libraries with much larger insert sizes (182 to 202 kb) for sequencing projects on humans and other organisms, including Arabidopsis, maize, and rice. The larger-insert libraries will provide significant improvement, he noted, to applications in physical mapping, positional cloning, and DNA sequencing.
Pieter de Jong (now at Parke-Davis Laboratory) also described new approaches to library construction and the preparation of new BAC vectors for BAC cloning and transformation-associated recombination (TAR) cloning. (See Web site for more information). When comparisons of multiple gene alleles are desirable, scientists use the TAR strategy invented by Natalay Kouprina and Vladimir Larionov (both at NIH National Institute of Environmental Health Sciences). TAR provides for an economical, selective recloning of target genomic DNA segments. The TARBAC variant has been used to prepare BAC libraries for several less-complex genomes of unicellular eukaryotes to model future work with mammalian TARBAC libraries.
UW and TIGR are generating sequence reads from BAC ends. These sequence tagged connectors (STCs) are useful markers that speed human genome contig building and sequencing. A target of one STC for every 3 kb of the human genome will eliminate bottlenecks in contig development. Beyond use in human genome sequencing, the characterized clones provide excellent resources for biological studies. The STC resource is available on the Web for use by any researcher for clone or sequencing target selection, and the clones can be ordered from commercial resources.
BAC-End Project Web Sites
The new "pZIP" plasmid vectors (named for the way the sequencing progresses along the insert) are maintained in a single-copy state that generally increases the stability of the foreign DNAs they carry and are amplified only when DNA is needed for sequencing. DNA segments up to at least 15 kb have been sequenced, and the reads have been assembled easily. Dunn's team currently is sequencing restriction fragments of human BACs with sizes in the 5- to 15-kb range.
Plasmid Unwinding For Sequencing
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Last modified: Friday, November 21, 2003
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