Finding Candidate Genes by Preparative in Situ Hybridization

We have developed preparative in situ hybridization (Prep-I.S.H.) of complex DNA populations to mitotic chromosomes as a means of generating chromosome region-specific cDNA subpopulations. Prep-I.S.H. is a combination of two cytogenetic techniques: hybridization of DNA molecules to mitotic chromosomes, and chromosome microdissection. Here we provide technical details of the procedure and describe its application to the human chromosome 11q22–23 region containing the ataxia telangiectasia genes. Prep-I.S.H. has a number of applications in studies of gene expression and genome organization, including efficient cytogenetic sorting of tissue-specific cDNAs and in dramatically reducing the number of candidate genes to aid in gene discovery. Prep-I. S.H. provides a technical approach to a “positional candidate” strategy for gene discovery that differs from positional cloning by focusing on analysis of the genes in a chromosomal region of interest rather than on detailed analysis of physical and genetic maps.