A faster DNA sequencing machine and streamlined analysis of the results can diagnose genetic disorders in days rather than weeks.
Up to a third of the babies admitted to neonatal intensive care units have a genetic disease. Although symptoms may be severe, the genetic cause can be hard to pin down. Thousands of genetic diseases have been described, but relatively few tests are available, and even these may detect only the most common mutations.
Whole-genome sequencing could test for many diseases at once, but its cost, the complexity of the results and the turnaround time are prohibitive. In what they hope will be a prototype for other hospitals, a research team led by Stephen Kingsmore at Children’s Mercy Hospital in Kansas City, Missouri, has implemented a much faster, simpler system for finding relevant mutations in whole-genome sequences that is designed for physicians without specialized genetic training.
These kinds of innovation will help more hospitals bring sequencing into clinical care, says Richard Gibbs, director of the human genome sequencing centre at Baylor College of Medicine in Houston, Texas. “A lot of people are going to realize from this that the future is now.”
Sequencing has been used before to pinpoint the cause of mysterious diseases. In 2011, Gibbs led a team that sequenced 14-year-old twins with a neurological movement disorder and found a way to improve their treatment2. In another instance, whole-genome sequencing suggested that a mysterious case of severe inflammatory bowel disease had a genetic cause and could be relieved through a bone marrow transplant3. But both these examples required several weeks and a team of experts to resolve. The Children’s Mercy Hospital plans to offer routine sequencing in the neonatal intensive care unit by the end of the year.
To order a test, physicians will choose terms from pull-down boxes to describe the infant's symptoms. Software then compiles a list of potential suspect genes. After the genome is sequenced, the software hunts for and analyses mutations in only those genes, which allows it to compile a list of possible causative mutations more quickly. The team had early access to a new DNA sequencing machine from sequencing company Illumina, based in San DIego, California, that could generate a whole genome within 25 hours. The entire process, from obtaining consent to preliminary diagnosis, took 50 hours, not counting the time taken to ship DNA samples and computer hard drives between Illumina's lab in the UK, where the DNA sequencing was carried out, and the hospital, where analysis was conducted. Kingsmore estimates that the cost of sequence and analysis is $13,500 per child, including costs to verify variants in a laboratory certified to perform clinical tests.
Fast sequencing cannot diagnose all genetic diseases. Current sequencing technology tend to overlook mutations such as duplicated genes, for example. Nonetheless, deep sequencing will be able to provide diagnoses for many cases that would otherwise remain harrowing mysteries.