? We have developed array CGH methodology for analysis of DNA copy number variations in the murine genome. Measurements of tumors from various cancer models have established the performance of the arrays, and the value of data they provide. Measurements employing an array that provides ~ 2 Mb resolution over the genome (~1500 BACs) found numerous DNA copy number polymorphisms among the standard mouse strains. The polymorphism may contribute to the strain-specific differences in phenotype and disease susceptibility that are exploited in cancer models. The rapid progress of the mouse genome project will allow us, in collaboration with the Vancouver British Columbia Genome Center, to produce an array containing a complete BAC tiling path of the mouse genome by the end of the current grant period. This array will contain about 30,000 clones. For the coming grant period we propose to use the whole genome tiling path array to comprehensively investigate DNA copy number polymorphisms among the mouse strains. This will include: ? ? 1. Validation of the performance of the tiling path array, including developing the informatics required to properly interpret the results. Validation will be accomplished through sequence analysis and hybridizations. In order to obtain specimens with a wide variety of copy number changes to test the arrays, and to collaborate with the MMHCC investigators, we will analyze ~1000 tumors from their various models. ? 2. Detection and mapping of copy number polymorphisms among mouse strains, and evaluation of their biological effects. We will use the tiling path array to map the polymorphisms by array CGH, characterize the genomic differences by sequence analysis, and carry out functional analysis as appropriate depending on the gene content of the regions. Comprehensive expression profiling will also be used to examine differences among the strains. New approaches for hybridization and analysis will be developed to extend the dynamic range of the expression measurements so we can obtain data from mRNAs expressed at very low abundances. ? ? ?
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