Appistry, a provider of HPC and analytics solutions for next-generation medicine, has partnered with the Undiagnosed Diseases Program (UDP) at the US National Institutes of Health (NIH) to implement a unique genetic-analysis pipeline for patient diagnosis.
Designed by the NIH and brought into production by Appistry, the pipeline analyses family genetics to narrow the search for genetic changes that underlie many rare and undiagnosed diseases. Rare diseases are defined in the US Orphan Drug Act as those that affect fewer than 200,000 individuals in the US. Of these individuals, just 150–170 qualify each year for the UDP.
‘Current methods compare an individual’s genome to a generic reference genome, which may differ significantly from the individual’s -- that creates an unnecessarily large number of possible genetic changes to pursue. Determining which changes are relevant is time-consuming and computationally intensive.’ said Dr William Gahl, director of the NIH UDP.
Appistry will help build a production-ready pipeline that uses an NIH UDP method of assembling and comparing genomes to identify changes that may be causing disease. In the method, a customised parental reference is assembled from the biological parents’ data and used to construct the child’s genome. The resulting trio of genomes is then compared against a standard reference to determine exactly where genetic variations exist. Processing first determines sites where the child’s genome differs from the parents’; a second pass determines which changes in the child’s genome are truly unique and not just missed during the first pass.