“…This has become the basic assumption since the Cre-loxP technology was first applied to conditionally express transgenes in mice in 1992 [1], [2]. In recent years, the use of loxP-containing transgenes in transgenic mice has increased but the possibility of unintended effects of this approach has not been taken into consideration [5], [7], [8], [9], [10], [11], [12], [13], [14], [37], [38], [39], [40], [41]. Our data demonstrate that, contrary to the widely held assumption that transgenes are integrated into the genome in a head-to-tail tandem array [5], [7], [8], [9], [10], [11], [12], [13], [14], [28], [29], [30], [37], [38], [39], [40], [41], inverted transgene integration is common when multiple copies of the transgene are integrated into the genome.…”