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.

Resource for Molecular Cytogenetics

C. Collins[2], L. Daneshvar[1], Karin Greulich[1], D. Kowbel[2], W.-L. Kuo[1], L. Riedell[1], F. Shadravan[2], D. Sudar[2], J. Mullikin[2], S. Lockett[2], P. Yue[1], U. Weier[2], Manfred Zorn[2], D. Pinkel[1,2], J. Gray[1,2]
[1]Dept. Laboratory Medicine, University of California, San Francisco, CA and [2]LBL National Laboratory, Berkeley, CA.

The LBL/UCSF Resource for Molecular Cytogenetics has been created to facilitate the application of molecular cytogenetics in clinical and biological studies. Work is being pursued in three areas: Development and application of improved hybridization technology, selection of probes optimized for use in fluorescence in situ hybridization (FISH), and development of digital imaging microscopy.

Work this year on hybridization technology has focused on development and application of comparative genomic hybridization (CGH), hybridization to thick tissue sections, and hybridization to extended single DNA molecules. CGH allows genome wide screening for DNA sequence copy number aberrations and has been applied in collaborative studies for characterization of whole chromosome and segmental aneusomies in prenatal specimens and in cancers of the breast, prostate, ovary, colon, bladder, lung, skin, brain, and blood. Progress also has been made on development of CGH using arrays of DNA sequences rather than metaphase chromosomes as the hybridization target. FISH to thick tissue specimens permits analysis of the genetic status of individual cells within the tissue architecture, for example permitting study of the genetic evolution of cancer. Hybridization to extended DNA molecules permits rapid determination of the positions of sub segments of a larger molecule, and measurement of the amount overlap of contiguous clones, among other applications.

Human probes for FISH have been selected from chromosome-specific cosmid libraries, YAC libraries and the Du Pont P1 library with primary emphasis on P1 clones. Our goal is to develop probes distributed at ~5 Mb intervals over the entire genome that contain STSs defining genes or genetically mapped polymorphic loci. To date, 233 such clones (218 P1's, 11 YACs and 4 cosmids) have been selected for 133 loci, including 40 genes. Selected clones are mapped according to FLpter using FISH. An additional 178 anonymous clones (75 P1's and 103 cosmids) have been selected at random and mapped. Included are probes for tumor suppressor genes and oncogenes (p53, c-MYC, GLI, SIS, E-Cadherin), translocation breakpoints of clinical significance (PML, RARA, TCRA, ETO, ALL), and regions involved in contiguous gene syndromes (Angelman, Prader-Willi, Cri du chat, Wolf-Hirschhorn and DiGeorge syndrome).

A QUantitative Image Processing System (QUIPS) has been developed in the Resource to facilitate molecular cytogenetic studies. Software currently allows multi-color image acquisition, chromosomal probe mapping (relative to the p-terminus), comparative genomic hybridization, metaphase finding three dimensional image display and computer assisted hybridization domain enumeration. Software for rare event scanning and three dimensional image segmentation and automated domain enumeration is under development.

Information about probes, technologies and software developed by the Resource will be available via an Internet Web Server and, when appropriate, through GDB.

(This work was supported by the US DOE contract DEAC0376SF00098 and Imagenetics)