57. Molecular Cytogenetics Comes of Age: A Resource that Extends From "T" to Shining "T"  

J. R. Korenberg¹, X. N. Chen¹, D. Noya¹, X.Wu², B. Birren², T. Hudson^2,3 
1 Medical Genetics Birth Defect Center, Cedars-Sinai Medical Center, University of California at Los Angeles, Los Angeles, California; ²Whitehead Institute, Massachusetts Institute of Technology, Massachusetts; and ³McGill University, Montreal, Canada 
jkorenberg@xchg.peds.csmc.edu 

With the maturation of the DNA sequence of the human genome, it becomes necessary to link this sequence to the language of clinical medicine. Therefore, to provide this bridge and at the same time, to anchor the genetic map to the chromosomal map, a genome-wide resource of bacterial artificial chromosomes (BACs) carrying defined Genethon polymorphic markers has been defined.  

Using PCR, 17,200 BAC DNAs were screened using a five-dimensional pooling scheme. Positives were confirmed by PCR, linked to a mapped BAC array and/or streaked and re-confirmed by FISH (fluorescence in situ hybridization) using fluorescence reverse banding at the 500-700 band stage. All data were recorded in a Fourth Dimension relational database and images archived on a gigabyte optical disc system. 

The resource is now represented by a BAC/STS map representing all human chromosomes, and includes 860 STS/BAC combinations, representing 882 total markers, each BAC mapping to a single chromosome sub-band. Of these 648 carry a Genethon markers, 84 carry ESTs, 42 carry known genes, 9 carry markers that were unmappable by any previous technique, and 108 carry random markers. A further 163 STS/BAC pairs mapped to one of multiple sites defined by FISH. Of the total 1122 marker/BAC pairs tested, 1023 of the chromosome assignments were in agreement; 99 were not. 

This framework resource uniquely provides integration with all existing maps. It anchors early sequencing, provides rapid access to cancer and prenatal breakpoints and their candidate genes, can map new genes to single bands without FISH when integrated with RH data, and can be used as targets for CGH (comparative genome hybridization) on slides, chips or filters. The resource integrates genome with genetics and medicine. It should speed solutions for diagnosis, prognosis and ultimately treatment. 

It may be viewed on http://www.csmc.edu/csri/korenberg/ and is available.