Clinical NGS

Several weeks ago, an infant in the neonatal intensive care unit at Children's Mercy Hospital in Kansas City, Mo., came to the attention of Stephen Kingsmore.

Kingsmore is executive director of the hospital's Center for Pediatric Medicine, and over the past several years, his lab has developed and refined methods for rapid genetic diagnosis of pediatric disorders using next-generation DNA sequencing technology. Using a high-speed run mode on the Illumina HiSeq 2500 and some clever computational algorithms that enabled geneticists to focus a variant search based on the patient's symptoms, his team showed in 2012 that it could return a genetic diagnosis from whole-genome sequencing in as little as 50 hours after sample receipt.

Now he was being asked to apply that method to a child who had to be kept on a ventilator, because he stopped breathing whenever he fell asleep. The condition is called "central hypoventilation syndrome," or "Ondine's curse," and according to Kingsmore, it is associated with multiple genes. The question was, which one?

To find out, the case was referred to Kingsmore. The child was enrolled on Friday afternoon, but samples weren't processed until the following Monday. By Wednesday, the sequencer had completed its run; at that point, automated software tools took over, identifying and ranking genetic variants based on their likely relationship to the disease. Thursday morning, when Kingsmore came into work, the data were ready for analysis. "Within a few minutes, I had the diagnosis," he says. The software had flagged a mutation in one of the genes initially deemed unlikely to be associated with the disease-"It was ranked No. 99 in terms of likelihood of causing the baby's features," Kingsmore notes-and the mutation's identification could help guide the child's treatment, or at least clarify difficult choices.