Human Genome Sequences Being Used in Diagnosis

Marisa Sloan
Staff Writer

PC: WP Paarz

A few years ago, it was difficult for pediatricians to anticipate which newborn babies would require emergency surgery. Now, the increased speed with which human genome sequences can be analyzed has led to life-saving diagnoses. Nathaly Sweeney, a neonatologist at Rady Children’s Hospital in San Diego and a researcher at Rady Children’s Institute for Genomic Medicine, spoke with NPR about how new technology is helping hospitals with their youngest patients.

“We just didn’t know whose heart was going to fail first,” said Sweeney. “There was no

rhyme or reason who was coming to the intensive care unit over and over again, versus

the ones that were doing well.”

At Rady, doctors were able to diagnose approximately two-thirds of sick newborns, but the remaining third would remain medical mysteries. With the new genome technology, pioneered by Rady’s Institute for Genomic Medicine, the genomes of over 1,000 babies have been successfully sequenced.

“We had patients that were lying here in the hospital for six or seven months, not

doing very well,” said Sweeney. “The physicians would refer them for rapid genome

sequencing and would diagnose them with something we didn’t even think of!”

At the Institute for Genomic Medicine, technicians use three sequencing machines, all worth one million dollars, to create a complete genome sequence from a baby’s DNA in as little as 16 hours. Then, through a process that used to take months, this sequence is analyzed by experts in a mere four hours thanks to newer and more sophisticated software. 

Kasia Ellsworth, one of the experts who analyzes the information, explained that she inputs a baby’s symptoms into the software, and waits for a list of genetic variants that may be related to the illness. About 40 percent of the time, the software is successful in selecting a viable genetic variation that doctors can then use to give a tentative diagnosis.

“We now are at the point where I think the evidence is overwhelming that a rapid genome sequence can save a child’s life,” said Dr. Stephen Kingsmore, the institute’s director.

While treatments are only available for a small percentage of the rare diseases being diagnosed, the information can still help parents and doctors to make educated decisions about what steps will be taken moving forward.

Kingsmore said the whole-genome test costs $10,000. Less expensive tests do exist, such as Invitae geneticist Dr. Ed Esplin’s genetic screen for epilepsy that costs only $1,500 and takes two weeks. However, Kingsmore said that because his test casts a wider net it has a higher likelihood of finding unexpected genetic variations. Additionally, because the sequencing takes significantly less time to reach a diagnosis, parents spend less money on intensive care unit stays.

“In some babies we avoid them being in the intensive care unit literally for months,” said Kingsmore. 

Some critics have argued that knowledge of genes and diseases evolves too rapidly the analyses to keep up with without missing a diagnosis. Dr. Isaac Kohane, chair of the department of biomedical informatics at Harvard Medical School, said that a typical person has 10 to 40 gene variants that textbooks incorrectly identified as causing disease.

“This is one of the few areas where I think the Human Genome Project is really beginning to pay off in health care,” said Kohane. “But buyer beware, it’s not something ready to be practiced in every hospital.”

Despite this, Kingsmore is pushing for more intensive care units to send their samples in for analysis. He hopes to reach 10,000 babies at hundreds of children’s hospitals.

“It’s going to be an incredibly exciting time in pediatrics,” said Kingsmore.

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