Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

EcoRI Restriction Mapping of Chromosome 19

Matt Burgin, Linda K. Ashworth, Stephanie Johnson, Laurie Gordon, Susan Hoffman, Anthony V. Carrano
Human Genome Center, L-452, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550.

The foundation chromosome 19 physical map is comprised of a set of overlapping cosmids clones assembled into contigs by automated fluorescence-based fingerprinting, which spans about 95% of the chromosome. Restriction mapping is being used to validate contig construction, close gaps between selected cosmid contigs, validate distance measurements obtained by FISH, and guide clone selection for genomic sequencing. Cosmids are digested to completion with EcoRI, and simultaneously ligated to a fluorescence-labeled oligomer. Fragments are separated using the PE/ABI 362 Gene Scanner. Fragment sizes are calculated by comparison to known fragments labeled with a different fluorophore and run in the same lane as the sample. Data are transferred directly to the chromosome l9 database. Restriction maps are assembled manually from the fragment data. Similar EcoRI mapping has been successfully done with BAC, PAC, fosmid, and P1 phage clones.

Over 170 restriction maps ranging from 45-1,020 Kbp have been assembled, representing coverage of approximately 60% (30 Mb) of the non-centromeric part of the chromosome. The maps span 87 genes and 137 genetic markers. In some cases, genes, markers or probes are associated with specific EcoRI fragments by southern hybridization. All restriction maps and associated hybridization data are displayed graphically using Browser and incorporated into the partial order map of the chromosome. Extension and consolidation of restriction maps is being directed in part by chromosome walking, and is aided by mapping larger insert clones when available.

This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract no. W-7405-ENG-48.