The present disclosure provides methods of generating multiplexedgenetically modified animals, for example, porcine endogenous retrovirus(PERV)-inactivaied pigs. The disclosure also provides methods of improving thebirth rate ofmultiplexed genetically modified animals. In some embodiments, the presentdisclosureis concerned with the generation and utilization of porcine cells in whichporcine endogenous retroviral (PERV) elements have been inactivated. In sonicembodiments,the PERV-free or PERV-reduced porcine cells are cloned to produceporcine embryos. In some embodiments, the PERV-free or PERV-reduced embryosmay be grown into adult swine from which organs and/or tissues may beextractedand used for such purposes as xenotransplantation into non-porcine animalssuchas humans.