With help from a health IT firm, the NIH’s Undiagnosed Disease Program hopes to make the sophisticated genetic analysis methods it developed to identify underlying causes of challenging diseases available to other institutions.
UDP has seen some 700 patients in the NIH’s Bethesda, Md., facility since it started back in 2008. These are patients with a longstanding medical condition that have stumped referring physicians.
Patients have to apply and be selected to be seen by the program’s expert staff. They undergo a week of vigorous testing that includes extensive phenotyping, next-generation sequencing and, sometimes, gene function analysis.
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In an attempt to find some answers for these patients, and to advance medical knowledge about the genes that underlie their rare diseases, UDP compares a patient’s genome to those of their family members.
A traditional genetic analysis would compare the patient’s data to a generic reference genome, explained Dr. William Gahl, clinical director of the UDP. But that generic reference genome may differ significantly from the individual’s, resulting in an unnecessarily large number of possible genetic differences to explore.
To narrow that search, UDP uses analytical programming it calls the diploid aligner to create a reference genome for each patient based on the genomes of the patient’s family members, which reduces the number of “false positive” gene candidates, Gahl said.
The program has been able to make somewhere around 70 diagnoses of very rare disorders, Gahl said, and in about 50 additional cases has identified candidate genes that may be associated with new diseases.
Now, St. Louis-based Appistry has been charged with scaling UDP’s programming and turning it into a commercial-grade product that other institutions could use.
Analyzing one genome or exome can be pretty complicated in itself, said Appistry CEO Kevin Haar. But in this case, UDP is comparing patient data against as much family data as they can get hold of. “An analysis for one patient ends up involving at least three people – that creates a very intense pipeline and lots of data and storage requirements,” he said.
Appistry, which has done something similar with the Broad Institute‘s inventions, will create the infrastructure to be able to offer the NIH’s diploid aligner as a cloud service for sequencing companies or research institutions.
“They take the rarest cases in the world and try to work to find solutions to those diseases,” said Haar. “Our hope is that we can do a lot to accelerate and build a community around that work.”
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