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.

Analysis of External YAC Data for Incorporation into the Chromosome 16 Map

R.D. Sutherland, R.M. Pecherer, L.A. Duesing, and N.A. Doggett
Center for Human Genome Studies, Los Alamos National Laboratory, Los Alamos, NM 87545.

Using our own chromosome 16 derived STS's and YAC pooling strategies, we have generated an STS-content map for 500+ mostly CEPH MegaYACs. The STS-content data that makes up this map is stored in our chromosome 16 relational database. Now that other laboratories have made their YAC, overlap-pair, STS, and primer data publicly available, we have incorporated this data into our database. We have taken advantage of the relational database structure to design complex queries to interrelate LANL and external data to expand coverage and close gaps in the 16 map. The starting point for STS-content mapping was a cosmid contig map covering 60% of chromosome 16 with 550 cosmid contigs (islands). STS's were developed from the largest of these contigs and used for somatic cell hybrid localization and PCR-based screening of CEPH MegaYACs. Single YAC bridges between islands could be produced directly from the STS content of YACs. Thus, a single YAC bridge exists when STS's from two different islands hit the same YAC. Using external YAC overlap-pair data (generated primarily from the fingerprinting of YAC clones at Genethon), we could evaluate double and triple YAC bridges between islands. A double YAC bridge occurred when two STS's hit separate YACs but these YACs directly overlapped. A triple YAC bridge occurred when two STS's hit separate YACs, each of which overlapped the same third YAC. This process could continue on but we felt farther reaches were too tenuous. These new bridges increased chromosome coverage and contributed to gap closure. Another benefit of using YAC overlap data is that this provided additional information for the ordering of STS's and YACs within breakpoint intervals of the somatic cell hybrid map. External STS-YAC data was easily integrated with our map because a) many of the external STS markers were already localized to the somatic cell hybrid map, and b) our cosmid-derived STS's and external STS markers hit common YACs. The STS data also identified candidate chimeric YACs i.e., hit by both chromosome 16 STS's and STS markers from other chromosomes. AluPCR data was used in conjunction with the STS data (eliminating YACs with STS hits on other chromosomes) to create a list of candidate YACs for further evaluation for their placement on 16.

Supported by the US DOE (W7405-ENG-36).