We have developed a strategy for the rapid enrichment and identification of cDNAs encoded by large genomic regions. The basis of this "direct selection" scheme is the hybridization of an entire library of cDNAs to an immobilized genomic clone or set of clones. Non-specific hybrids are eliminated and selected cDNAs are eluted. These molecules are then amplified and are either cloned or subjected to further selection/amplification cycles. The feasibility of this selection strategy has already been demonstrated and it is capable of enriching low abundance cDNAs by up to 2000-fold in one selection cycle. We shall further develop the sensitivity and selectivity of this scheme by optimizing conditions for additional cycles of enrichment and by depleting highly repetitive elements from cDNA libraries. Multiplexing schemes will be developed in which several cDNA libraries will be separately "tagged" and selected as a group, allowing the source of each derived cDNA to be determined after the selection. We shall apply these improved methodologies to the selection of chromosome 5-specific cDNA libraries from four separate tissues. One hundred of these cDNAs will be converted to sequence tagged sites and will be positioned within the physical map of chromosome 5. This technique for identifying coding regions in genomic DNA should be useful for the rapid isolation of large numbers of cDNAs, including disease-related genes, across extensive portions of the human genome.