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.

Application of Fluorescence in situ Hybridization in Genome Analysis

Barbara J. Trask[1], Hiroki Yokota[1], Cynthia Friedman[1], Hillary Massa[1], Eric Green[2], Jim Evans[3], Antonia Martin-Gallardo[4], Janey Youngblom[5], and Ger van den Engh[1]
[1]University of Washington, Seattle, WA; [2]National Center for Human Genome Research-NIH, Bethesda, MD; [3]University of North Carolina, Chapel Hill, NC; [4]Centro Nacional de Biotecnologia, Madrid, Spain; [5]California State University, Turlock CA.

We report on the application of fluorescence in situ hybridization (FISH) to several areas of genome research:

A) Correlating and confirming maps. The extensive cross-correlation of the cytogenetic map with the genetic and physical maps of chromosome 7 will be shown as an example.

B) Mapping relative to chromosome rearrangements. This application will be illustrated with results on patients with split-hand/split-foot syndrome. YACs from 7q were ordered by FISH relative to deletion and translocation breakpoints in 10 patients. The results order the breakpoints along the chromosome and demonstrate that the critical region for this disease spans 500 kbp.

C) Characterizing large-scale polymorphisms. We have characterized a 40-kbp region in different individuals by a combination of FISH, PCR, and hybridization to flow-sorted chromosomes. This sequence is found near the ends of several human chromosomes, but on only one chimp or gorilla chromosome. The region is polymorphically present on additional chromosomes in some individuals. The frequency of polymorphic variants differs among reproductively isolated populations. Limited sequencing indicates that the region may contain functional genes.

D) Studying the organization of the interphase nucleus. We have made >25,000 pair-wise distance measurements in G1 interphase nuclei between DNA sequences separated by 0.15 to 190 Mbp on three different human chromosomes. Our results are consistent with a model in which interphase chromatin is organized in ~5-Mbp-sized flexible loops held together along a supple backbone-like structure. The results have important consequences for the use of FISH as a mapping tool.

This work was funded by the U.S. DOE grant FG06-93ER61553, B. Trask, P.I.