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Many rare genetic conditions have effective interventions; however, without timely implementation, these conditions can progress to severe morbidity and even mortality. For the most relentlessly progressive conditions, a rapid molecular diagnosis alone is not sufficient to improve outcomes in these conditions. Frontline physicians are frequently unfamiliar with many of these conditions and their treatments. Additionally, the field of genetics is rapidly expanding and new conditions along with new interventions are being increasingly described. Here we present a review of the development and use of two linked automated systems developed to help overcome this problem. The first, GTR X (gene to treatment) has been developed to assist with the management of the acutely ill neonate infant or child in the neonatal or pediatric intensive care unit found to have a recognized genetic disease. Subsequently with expansion of newborn screening to potentially involve rapid next generation sequencing of newborns in parallel with the current analyte based newborn screening, we have developed an additional system, BeginNGS, intended to be used with currently available ACTion (ACT) sheets that will address both recommended confirmatory testing and initial interventions, particularly focusing on conditions that are not amenable to conventional newborn screening.