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.

Construction of a P1 Map in the Region of Chromosome 5q31-q35

Jan-Fang Cheng, Steve Lowry, Yiwen Zhu, Duncan Scott and Eddy Rubin
Human Genome Center, Life Science Division, Lawrence Berkeley Laboratory, MS 74-157, 1 Cyclotron Road, Berkeley, CA 94720

The mapping project at the LBL Human Genome Center has focused on generating a set of P1 clones providing a complete coverage of the target region so that cloned genomic fragments with minimal overlaps can be determined and selected as templates for production sequencing. The q31-q35 region of chromosome 5 was chosen as the primary target for sequencing because this region contains a cluster of growth factor or receptor genes and it is likely to yield new and functionally related genes through long range sequence analysis. We have selected the 1.1 Mb interleukin gene cluster region in 5q31 as a starting point because: (l) that it contains a number of genes with related biological function, therefore, it exists the high likelihood that other genes resulting from gene duplications will be identified through sequence analysis; (2) that the genes localized to this region are of considerable health and medical importance. The known genes regulate hematopoietic cell proliferation; (3) the fact that multiple, previously sequenced genes (IL3, IL4, IL5, IL13, IRF1 and CSF2) are dispersed throughout this region would serve as a quality control for production sequencing; (4) the fact that sequence and functional information about the genes already characterized from this region may well assist in the difficult task of assigning importance and function to genes derived from the production sequencing program.

There are three key experimental steps in our mapping strategy, and they were designed to generate a clone map for specific regions of a chromosome in a time- and cost-effective way. The first step is to use inter-Alu fragments generated from YACs to isolate regionally specific P1s covering the target region. The second step is to establish the order and overlaps of the isolated P1s in a clone-limited approach. The third step is to close gaps and verify the integrity of the cloned fragments.

Three non-chimeric YACs were identified to spin the 1.1 Mb interleukin gene region, and 54 P1s have been isolated using probes derived from these YACs. Informative STSs were developed from 6 known genes and l9 ends of key P1s to resolve two contigs (700 Kb and 300 Kb in size). DNA sequences flanking the gap are being used to identify additional clones for closure. All STSs are being used to generate restriction maps from both genomic DNA and cloned DNA in this region. The restriction map comparison should allow us to identify gross structure rearrangement, if any, in the cloned P1 DNA.