Combined DNA probe sets will be developed which allow the simultaneous detection of disease specific chromosomal aberrations by multicolor fluorescence in situ hybridization.
Following optimization of single probes, diagnostic probe combinations are designed for acute lymphatic and myeloid leukemias as well as for chronic lymphoid leukemias and other types of malignant lymphomas. In addition to the known specific chromosome aberrations, numerous cases of these diseases are found to show no chromosomal changes.In order to analyze the genomic imbalances in these diseases on a new level, we will apply the approach of comparative genomic hybridization (CGH, see below).
Genomic DNA from cell populations highly enriched in tumor cells is hybridized in situ to metaphase chromosomes from normal individuals. Above a general chromosomal staining, DNA sequences overrepresented in the tumor genome result in a stronger and underrepresented sequences in a weaker staining of the corresponding regions.
For the aberrations newly defined by CGH, DNA probes will be included in the disease specific probe combinations.
The diagnostic potential of these probe sets will then be tested using cytogenetically characterized patient cells followed by a blind study. The optimized probe sets should provide a basis for the automated analysis of chromosomal aberrations in leukemias and lymphomas.
The ideal probe for the detection of a deletion would consist of the whole genomic DNA present in the targeted chromosomal region.
We propose to elaborate techniques for a new strategy which would allow the generation of region specific DNA probe pools suitable for the diagnosis of even microdeletions: Highly extended chromatin fibers (Heng et al., 1992) prepared from normal individuals will be used for CGH to develop a technique for the delineation of disease specific deletions at a very high resolution.
It is planned to elaborate a microdissection technique allowing the physical isolation of the corresponding genomic material from such fibers.
Following amplification by universal PCR (Telenius et al.,1992) these sequences could be used i) to probe for the corresponding aberration in patients, ii) to be integrated as an optimized probe into the multicolor probe sets and iii) to probe YAC and cDNA libraries in order to isolate the complete sequences from this genomic region or disease candidate genes, respectively.
This technology development will be conducted using DNA from renal cell carcinomas with well defined deletions in 3p and could be extended using DNA from leukemia cells.
Funding SchemeCSC - Cost-sharing contracts
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