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Sponsored
by the U.S. Department of
Energy Human Genome Program
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DOE Human Genome Program Contractor-Grantee Workshop IV
Santa Fe, New Mexico, November 13-17, 1994
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Introduction to the Workshop
The electronic form of this document may be cited in the following style: Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected. |
A Metric Physical Map of Human Chromosome 19Linda K. Ashworth, (ashworthl@llnl.gov), Joe Balch, Mark Batzer, Brigitte Brandriff, Elbert Branscomb, Emilio Garcia, Jeff Garnes, Jeff Gingrich, Jane Lamerdin, Richard Langlois, Greg Lennon, Ray Mariella, Harvey Mohrenweiser, Anne Olsen, Tom Slezak, and Anthony V. Carrano The chromosome 19 physical map constructed at Lawrence Livermore National Laboratory is a high resolution cosmid-based map spanning the entire chromosome. The foundation of the map consists of a set of 802 cosmid contigs assembled by an automated restriction fragment fingerprint analysis of cosmids from a chromosome 19-specific library. These contigs span an estimated 54 Mb, or >95% of the chromosome excluding the centromere. Over 400 of the contigs have been mapped by fluorescence in situ hybridization (FISH) to metaphase bands. About 160 contigs have been further ordered along the chromosome by a high resolution FISH mapping technique in which the distance between cosmid markers is also determined (see poster by Brandriff, et. al). This ordered FISH map provides a 'to-scale' framework, or metric map, upon which to anchor cosmid contigs. By identifying large insert clones (YACs, BACs, PACs and P1s) that span gaps between the ordered cosmid contigs, we have decreased the number of ordered islands to 72. These islands cover a cumulative length of 38 Mb, or about 75% of the non-centromeric part of the chromosome, with the largest island spanning over l0 Mb (see poster by Elliott, et. al.). YACs are isolated by either of two procedures: STS screening of total genomic YAC libraries or hybridization of Alu-PCR products from cosmid contigs to Alu-PCR products from a chromosome 19-enriched YAC sub-library provided by Genethon. Large insert clones spanning gaps are being hybridized back to the cosmid library to identify additional cosmids/contigs located in the gaps. Overlap between adjacent contigs in these regions can often be determined by EcoRI mapping. In some cases cosmid walking experiments are needed in order to achieve continuity at the cosmid level. To date, over 30 Mb of EcoRI restriction maps have been generated (see poster by Burgin, et. al.). In addition, over 400 genes and genetic markers have been localized on cosmids, of which nearly 300 have been incorporated into the metric map (see poster by Tsujimoto, et. al.). Genomic sequencing is being done in selected regions of interest (see poster by Lamerdin, et. al.), particularly on three DNA repair genes found on the chromosome. Software has been designed (see poster by Wagner, et. al.) that integrates and displays cosmid, YAC, FISH, and restriction maps, as well as sequence, hybridization, and screening data. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory, contract no. W-7405-ENG-48.
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