During IVF procedures pre-implantation genetic diagnosis (PGD) allows for genetic profiling of embryos prior to replacement. Most PGD procedures during IVF are performed to select chromosomally normal embryos as comprehensive chromosome screening (CCS), and in a smaller number of cases PGD is used for embryo selection against known genetic disease variants carried by the parents. Genomic technologies utilizing PCR, microarray, and second-generation sequencing methods are currently being used for PGD data analysis in the laboratory. With decreasing costs in second-generation sequencing technologies coupled with increased demand for PGD, adoption of "PGD-seq" methods for CCS and genetic selection will face significant future challenges in data management, analysis and information delivery to clinicians. One of our goals is to provide secure, integrated environments for clinicians to use genetic information to inform treatment strategies. I discuss challenges and strategies for storing and integrating biomedical data with other private and public data repositories. I discuss process and warehouse design, analysis methods and implementation strategies for PGD and genetics data. I discuss how we deliver and visualize PGD data for clinicians and to researchers in clinical and basic science.