“Sequencing is just a small part of it,” adds Sarah Murray, a director of genetics at the Scripps Translational Research Institute. “There is insurance, billing, ethics.” For example, should scientists reveal genetic mutations that don’t underlie the disease at hand but might put the patient at particular risk for other disorders later in life? (Jacob’s team specifically asks families what they want to know from the genome sequence. They can change their minds at any time.)
The team’s most recent success: an unidentified insurance company has said it will cover sequencing costs in cases where the team can demonstrate that it is likely to be cheaper than the typical string of diagnostics. Children with rare diseases often go through a series of tests each of which search one or a few genes for the mutation causing the disease. Exactly how much the center will bill insurance companies is still up in the air, in part because the cost is dropping so rapidly. The time it takes to analyze a genome, a factor in cost, has dropped from a few months to a few weeks. Jacob says he expects to analyze about 20 genomes this year and 100 next year.
The center focuses on patients with rare single-gene diseases and a unique set of symptoms. And it takes only cases in which the researchers think sequencing will help the patient, rather than those that might be interesting purely for research purposes. The DNA is sent to Illumina, a genomics technology company whose sequencing lab has been clinically certified by the Food and Drug Administration. Patients don’t have to pay for sequencing; what isn’t covered by insurance is paid for with philanthropic funding from the center.
Thus far, the team has analyzed the genomes of five children and has another seven on the docket. In two of the first five, the researchers believe they identified a genetic mutation that helped the physician make choices about the patient’s treatment. In one case, sequencing revealed that the child would not benefit from a liver transplant, thus saving the liver for another recipient.
Scientists now broadly agree that reading the sequence of DNA is the easy part of genome analysis; figuring out what the sequence means is the real challenge. To help automate that portion of the process, the Wisconsin team has developed software that flags mutations of interest and combs genetics databases for their potential meaning. Jacob says the center hasn’t yet decided whether to market this software or make it freely available to the genetics community.
Hear more from Illumina at EmTech 2014.