DOE Contractor-Grantee Workshop Mapping Sessions

Chromosome 16.

Norman Doggett (LANL) summarized the 5-year chromosome 16 mapping effort that resulted in an integrated physical-genetic-cytogenetic map. A high-resolution (1-Mb) cytogenetic breakpoint map provided the framework for constructing all levels of the integrated map. The physical map consists of both a low-resolution (0.25-Mb) YAC contig map and a high-resolution (38 Mb) of the chromosome has already been defined to the level of EcoR I restriction sites. The group has also assigned genes, cDNAs, STSs, polymorphic markers, and ESTs to the map. Overall coverage is about 1 marker per 147 kb, with the goal of 1 marker per 100 kb .

Future LLNL plans outlined by Harvey Mohrenweiser include (1) in collaboration with Oak Ridge National Laboratory (ORNL), construction of a complete high-resolution transcript map of chromosome 19 and genomic regions of special interest in both and mouse; (2) continued development of high-throughput sequencing methods and technologies and sequencing of selected human and mouse genomic regions; and (3) application of resources and techniques to relevant issues in disease susceptibility, biological structure and function, and environmental sciences.

Tom Slezak noted challenges in providing informatics tools to support mapping efforts at LLNL, including automation of as much map construction and integration as possible and construction of flexible tools to handle multiple viewpoints and allow scaleup. He emphasized the importance of active support and participation by biologists in design. Future challenges include building informatics tools to support sequencing, expanding the system to query and navigate across multiple chromosomes and species, actively participating in the federation of genomic databases, and expanding external collaborations.

Lisa Stubbs and Richard Woychik (ORNL) discussed the mouse as a model system for predicting and identifying genes in humans and for studying gene function. Stubbs reported on collaborative efforts with LLNL that have revealed striking similarities between sections of mouse chromosome 7 and human 19. Woychik stressed the importance of developing a high-throughput transgenic and targeted mutagenesis strategy in mice to accommodate the future study of health effects caused by genes identified through human genome mapping.

Chromosome X.

David L. Nelson (Baylor College of Medicine) discussed use of LLNL flow-sorted cosmids to increase resolution of the X chromosome short-arm YAC map; he believes these cosmids will become common currency for exchanging X chromosome mapping information. His group is using WWW-based browsers entering, annotating, and correcting information. Nelson stressed the need to develop joint databases that provide researchers worldwide with access to information on each flow-sorted chromosome library.

 DOE Contractor-Grantee Workshop Mapping Sessions

Chromosome 16.

Norman Doggett (LANL) summarized the 5-year chromosome 16 mapping effort that resulted in an integrated physical-genetic-cytogenetic map. A high-resolution (1-Mb) cytogenetic breakpoint map provided the framework for constructing all levels of the integrated map. The physical map consists of both a low-resolution (0.25-Mb) YAC contig map and a high-resolution (38 Mb) of the chromosome has already been defined to the level of EcoR I restriction sites. The group has also assigned genes, cDNAs, STSs, polymorphic markers, and ESTs to the map. Overall coverage is about 1 marker per 147 kb, with the goal of 1 marker per 100 kb .

Future LLNL plans outlined by Harvey Mohrenweiser include (1) in collaboration with Oak Ridge National Laboratory (ORNL), construction of a complete high-resolution transcript map of chromosome 19 and genomic regions of special interest in both and mouse; (2) continued development of high-throughput sequencing methods and technologies and sequencing of selected human and mouse genomic regions; and (3) application of resources and techniques to relevant issues in disease susceptibility, biological structure and function, and environmental sciences.

Tom Slezak noted challenges in providing informatics tools to support mapping efforts at LLNL, including automation of as much map construction and integration as possible and construction of flexible tools to handle multiple viewpoints and allow scaleup. He emphasized the importance of active support and participation by biologists in design. Future challenges include building informatics tools to support sequencing, expanding the system to query and navigate across multiple chromosomes and species, actively participating in the federation of genomic databases, and expanding external collaborations.

Lisa Stubbs and Richard Woychik (ORNL) discussed the mouse as a model system for predicting and identifying genes in humans and for studying gene function. Stubbs reported on collaborative efforts with LLNL that have revealed striking similarities between sections of mouse chromosome 7 and human 19. Woychik stressed the importance of developing a high-throughput transgenic and targeted mutagenesis strategy in mice to accommodate the future study of health effects caused by genes identified through human genome mapping.

Chromosome X.

David L. Nelson (Baylor College of Medicine) discussed use of LLNL flow-sorted cosmids to increase resolution of the X chromosome short-arm YAC map; he believes these cosmids will become common currency for exchanging X chromosome mapping information. His group is using WWW-based browsers entering, annotating, and correcting information. Nelson stressed the need to develop joint databases that provide researchers worldwide with access to information on each flow-sorted chromosome library.