Background: Genetically engineered mouse models are critical tools to study the genetics and pathogenesis of Alzheimer’s disease (AD), and are widely used in preclinical research. The Jackson Laboratory AD resource provides a large set of strains expressing mutant forms of human APP, MAPT (tau), APOE, Baces, Presenilins, and other relevant genes, as well as information supporting their selection and usage. All strains are rederived to a high health status, and genetic quality control measures are used to verify the strain’s genetic background and the presence of the human allele. Here we describe our efforts to expand genetic quality control by using high throughput sequencing for transgene insertion site discovery. We are also expanding the resource to include in vitro tools for AD research. Here, we describe the development of novel ES cell lines from some of our most widely utilized AD strains.Methods: To identify transgene insertion sites, we are using high throughput sequencing of mate pair libraries and a novel analysis pipeline to identify transgene insertion sites. To develop novel ES cell lines, we are using well-established ES cell derivation techniques and have introduced a tau promoter driven GFP transgene to provide a marker for neuronal differentiation. Results: To date the transgenic integration events in the “5XFAD”, “APP/PS1”, and “3xTg-AD” strains have been defined and are currently being validated. In addition, we have now generated ES cell lines from “5XFAD”, “APP/PS1” and “J20” models and we are currently testing the capacity of these ES cells for neuronal differentiation.Conclusions:Many of the most widely cited mouse models are currently available through The Jackson Laboratory AD resource, and we continue to maintain the genetic integrity of these models and to expand the resource according to the needs of the AD research community. Our transgene insertion site data enable us to determine whether insertion sites disrupt genomic sequences that are physiologically relevant, and to develop simplified genotyping assays. The ES cells we are creating will provide in vitro tools for the study of neuronal phenotypes related to over-expression of human AD genes. Detailed strain, ES cell, and availability information can be found at http://research.jax.org/grs/alzheimers.html