The technology uses pre-selected frequent cutting restriction enzymes and proprietary linkers to produce smaller amplicons that, in practice, reduce the bias effects of other more commonly used mapping techniques that often include linear amplification as a first step. Further, the technology does not require the use of measurable phenotypic characteristics to analysis or distinguish integration events. Thus, knowledge of potential cellular changes is not required. This invention can be used to provide rapid, cost-effective screening of cells treated with retroviruses for gene therapy. The ability to identify potentially harmful integrations and eliminating them from therapeutic use is essential for safer gene therapy applications.