We have developed a gene transfer approach to facilitate the identification and isolation of chromosomal regions which are prone to high-frequency gene amplification. Such regions are identified by assaying for transformants which show high-frequency resistance to PALA and/or methotrexate by amplification of a vector containing the genes which encode the enzyme targets of these antiproliferative agents. We identified 2 of 47 transformants which displayed high-frequency amplification of the transfected genes, and in this report we describe the analysis of one of them (L46). Molecular analysis of the integration site in transformant L46 revealed that the donated genes were at the center of an inverted duplication which spanned more than 70 kilobase pairs and consisted largely of host DNA. The data suggest that integration of the transfected sequences generates a submicroscopic molecule containing the inverted duplication and at least 750 kilobases of additional sequences. The donated sequences and the host sequences were readily amplified and lost in exponentially growing cultures in the absence of drug selection, which suggests that the extrachromosomal elements are acentric. In contrast to the instability of this region following gene insertion, the preinsertion site was maintained at single copy level under growth conditions which produced copy number heterogeneity in L46. The implications of our results for mechanisms of genetic instability and mammalian gene amplification are discussed.Gene amplification, a localized increase in DNA sequence abundance, is one mechanism by which a cell or organism can increase the level of a gene product required for continued cell function or survival. Examples of amplification have been described in organisms as diverse as bacteria (1), plants (42), insects (10), and humans (53). The numerous examples of gene amplification indicate that many regions of the genomes of these organisms are susceptible to molecular remodeling by this process (for reviews of amplification mechanisms, see references 3, 9, 20, 41, and 44).To examine the molecular mechanisms of mammalian gene amplification, we have developed gene transfer systems which enable us to scan the genome for sites which facilitate amplification (48, 51). The generation of cell lines which amplify transfected drug resistance genes at frequencies higher than 10-3 facilitates the molecular characterization of the initial events of amplification. One example of the usefulness of this approach is provided by our previous studies with a transfected CAD gene which revealed previously unsuspected intermediates in the amplification process. These intermediates, called episomes, have been shown to be submicroscopic autonomously replicating circular precursors of double minute chromosomes (DMs), the typical cytogenetic structures associated with extrachromosomal gene amplification in mammalian cells (7,8,51 In this paper we report the molecular and cellular characterization of one transformant, L46, which exhibited highfrequency ampl...