PNRI’s Dudley Lab has developed an experimental framework to accurately measure the functional impact of genetic variation in human protein coding sequences on a scale sufficient to analyze individual alleles and allele combinations comprehensively. The approach leverages large-scale gene synthesis and high throughput in vivo assays of protein function in model organisms, such as yeast. Engineering the system such that the results in a model organism accurately reflect the protein’s function in humans is critical to the success of these studies. To achieve this, the lab collaborates closely with clinicians and disease experts.
The Dudley Lab is applying these methods to a several metabolic diseases, including a set of rare diseases called urea cycle disorders (UCDs). UCDs result from inherited deficiencies in any of the eight proteins in the urea cycle. Infants with neonatal onset often appear healthy at birth but rapidly develop high levels of ammonia and cerebral edema that can progress to coma and death. Hyperammonemia in newborns initially presents with nonspecific symptoms that often appear after discharge from the hospital. Despite the availability of potentially lifesaving interventions such as dialysis and nitrogen scavenging drugs to reduce ammonia levels, only ~60% of early onset patients survive the neonatal period, 19% of these die within the first year of life, and most survivors have neurological damage. While timely diagnosis is key, limitations of the biochemical assays for several UCDs have precluded their use in newborn screening.
Whole exome or genome sequencing has the potential to substantially increase the positive impact of newborn screening, and pilot programs are currently evaluating its real-world implementation. By providing quantitative data on the functional impact of thousands of variants, the lab’s results are filling critical unmet needs that will improve the diagnosis and treatment of these devastating diseases.
