Rapid whole genome sequencing has the potential to save lives and prevent permanent brain and organ damage in infants.
Rapid whole genome sequencing can analyze genetic information to identify possible genetic causes of diseases that if left untreated can lead to permanent damage and even death in infants and babies. Rady Children’s Hospital in San Diego is using this technology in its genomics institute, which was founded by internist Stephen Kingsmore in 2014.
Kingsmore set a Guinness world record in February 2018 for sequencing a genome in 19.5 hours. Standard genomic testing methods take four to six weeks to complete. In many cases, infants will die in that time without proper treatment. He would like to see rapid genomic sequencing be standard care in all neonatal intensive care units.
His team at Rady conducted a study with 42 infants comparing traditional and rapid sequencing methods in the diagnosis of their diseases, which all were suspected to have a genetic basis. The standard method identified a disease in just four cases, while the rapid method found an answer in 18 infants. Eleven of those babies received lifesaving surgeries or medications.
Another study conducted in part by Josh Petrikin, a neonatologist at Children’s Mercy Kansas City, was halted half-way through because the evidence supporting the use of rapid sequencing was too compelling to continue with the randomized trial. “If you as the investigator truly believe that one technology arm is superior to the other, then it may become unethical to still randomize and deprive half the patients from it,” Petrikin said.
One current challenge is cost. In the Rady study, however, the treatment of six of of the infants with quicker diagnoses was estimated to save $800,000 – more than the $675,000 it cost to do the rapid sequencing for all 42 babies. “We did this study to show better outcomes for patients but also to show it’s economically feasible,” says study co-author Lauge Farnaes, a pediatric hematologist-oncologist at Rady. “It’s a win-win.”
Another issue is the limited availability of real-world evidence that is needed for insurance companies to cover rapid genome sequencing for infant disease diagnosis. “Rapid whole genome sequencing is still considered investigational, and payers don’t want anecdotal evidence. The bigger question is whether there’s solid evidence that when the technology is applied in practice there’s widespread benefit,” noted Scott Grosse, who researches health economics at the Centers for Disease Control and Prevention.
There is also a need to determine which infants will most benefit from rapid genome sequencing, because not all will. Some will be terminally ill and others will have diseases with not available treatments. “Anytime you have a new technology, you have to determine who might benefit from a cheaper test,” said Kathryn Phillips, who studies health-care technology at the University of California at San Francisco.
Others argue that putting a dollar figure on disease diagnosis for infants is not reasonable. Even if parents find out their child cannot be treated, they have that knowledge rather than uncertainty. Rapid sequencing can also eliminate the need for unnecessary testing. And in cases where the baby is terminal, parents are given time to prepare. Perhaps most importantly, for babies with diseases that are treatable, a lifetime of suffering - and healthcare costs – can be avoided.
Fortunately, the cost of rapid genome sequencing is decreasing at a steady pace. For instance, the company Illumina recently introduced the NovaSeq instrument, which company CEO Francis deSouza claims could ultimately reduce the price for sequencing down to $100 from $1000 currently (and $300,000 in 2006).
In the meantime, Kingsmore is partnering with over children’s hospitals throughout the US, proving analysis to infant blood samples that are shipped to San Diego overnight.