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.

Reagents For Understanding And Sequencing The Human Genome

[1]J. R. Korenberg, [1]X.N. Chen, [1]S. Gerwehr and
BAC: [1]S. Mitchell, [1]R. Hubert, [2]U.-J. Kim, [2]H. Shizuya, [2]M. Simon, [1]K. Yamakawa.
cDNA: [3]M. Adams, [4]K. Becker, [5]K. Denison, [4]P. Drew, [5]J. Gatewood, [6]G. Guellaen, [7]L. Hood, [8]D. Hwang, [7]G. M. Huang, [8]C.-C. Liew, [3]J. C. Venter
[1]Cedars-Sinai Medical Center & UCLA, Los Angeles, CA; [2]California Institute of Technology, Pasadena, Ca.; [3]Institute for Genomic Research, Gaithersburg, MD; [4]Neuroimmunology Branch, NINDS; [5]Los Alamos National Laboratory, Los Alamos, NM; [6]INSERM U 99 Hospital Henri Mondor 94010. Creteil, France; [7]University of Washington - Seattle, Wa; [8]University of Toronto, Canada.

An ultimate goal of the human genome project is to rapidly identify a subset of the 50-100,000 human genes that is responsible for genetic and acquired disease. Toward this goal, we have focused work in two areas: defining and mapping the genes and providing arrays of genomic reagents for gene finding, sequencing and molecular cytogenetics.

I. Human cDNA Mapping using Fluorescence in situ Hybridization (FISH)
Technology has been developed and applied for the rapid assignment of cDNAs to single sub-bands (2-6 Mb regions) of high resolution human chromosomes. An international consortium of 6 groups has been established and has resulted in the mapping of 240 new genes from 5 tissue-specific cDNA libraries to single human chromosome regions. These include testis, fetal brain, fetal and adult heart, bone marrow, and prostate, in addition to members of the family of zinc finger-motif-containing genes. The techniques developed eliminate the confusion of pseudogenes, confirm and provide anchor points for the large fragment maps, and rapidly and unambiguously provide candidate genes for diseases mapped in the region. Further, the throughput would allow low-cost (<$100) assignment of 8-10,000 genes in 3 years by a single production group.

II. Towards a BAC Map of the Human Genome
Although the construction of YAC libraries has clearly changed the paradigm for generating complete genome arrays, there is a basic, widespread need for large fragment stable reagents covering the genome. To address this need, the laboratory has begun the elaboration of a genome-wide array of BACs using a random, cost-efficient strategy to obviate the issues of YAC chimerism and rearrangement. The ultimate goal is to provide stable reagents for 70% of the genome. These arrays would be produced by using current techniques of multiplex FISH to assign 24-30,000 BACs to genomic regions at a resolution of 2-6 Mb. This resource will provide unambiguous reagents for gene identification and sequencing, will fix the cytogenetic to the molecular maps, are readily integrated by STS and hybridization analyses within a 2-5 Mb region and provide anchor points for generating complete contigs, easily combined with other large-fragment libraries including YACs, PACs, P1s, cosmids, and fosmids. Toward this goal, we have assigned more than 1,000 BACs, that cover more than 80% of all chromosome bands and have identified a subset of 148 BACs containing chromosome-specific human alpha-satellites and have identified BACs for 7 human telomeres. Chimerism in the library has been evaluated and estimated at less than 5%. These reagents now provide a broadly accessible resource for rapidly generating contigs of any genomic region, allowing the study of human centromeres and telomeres, and facilitating the pace of human gene discovery. This requires knowledge of the cDNAs and their map positions, an array of stable genomic reagents that cover most of the genome and are suitable for sequencing, and a high resolution genetic map. The goal of the research in this laboratory has been focused on characterizing the cDNAs and providing their potential relationship to human genetic disease.