Just 48 hours after her birth in a Seattle-area hospital in 2021, Layla Babayev was undergoing surgery for a bowel obstruction.
Two weeks later, she had another emergency surgery, and then developed meningitis. Layla spent more than a month in neonatal intensive care in three hospitals as doctors searched for the cause of her illness.
Her parents enrolled her in a clinical trial to check for a genetic condition. Unlike genetic tests focused on a few disease-causing variants that can take months to produce results, the study at Seattle Children’s Hospital would sequence Layla’s entire genome, looking for a broad range of abnormalities — and potentially offer answers in under a week.
The test found Layla had a rare genetic disorder that caused gastrointestinal defects and compromised her immune system. The findings led doctors to isolate her, give her weekly infusions of antibiotics, and contact other hospitals that had treated the same condition, said her father, Dmitry Babayev.
Today, Babayev credits the test, known as rapid whole-genome sequencing, for saving his daughter’s life. “It is why we believe Layla is still with us today,” he said.
Like her disorder, Layla’s experience is rare.
Few hospitalized babies with an undiagnosed illness undergo whole-genome sequencing — a diagnostic tool that allows scientists to quickly identify genetic disorders and guide clinicians’ treatment decisions by analyzing a patient’s complete DNA makeup. That’s largely because many private and public health insurers won’t cover the $4,000-to-$8,000 expense.
But an alliance of genetic testing companies, drugmakers, children’s hospitals and doctors have lobbied states to increase coverage under Medicaid — and their efforts have begun to pay off.
Since 2021, eight state Medicaid programs have added rapid whole-genome sequencing to their coverage or will soon cover it, according to GeneDX, a provider of the test. That includes Florida, where the Republican-controlled legislature has resisted expanding Medicaid under the Affordable Care Act.
The test is also under consideration for coverage in Georgia, Massachusetts, New York and North Carolina, according to the nonprofit Rady Children’s Institute for Genomic Medicine, another major provider of the test.
Medicaid coverage of the test can significantly expand access for infants; the state-federal program that insures low-income families covers more than 40% of children in their first year of life.
“This is an extraordinary, powerful test that can change the trajectory of these children’s diseases and our own understanding,” said Jill Maron, chief of pediatrics at Women & Infants Hospital in Providence, Rhode Island, who has conducted research on the test.
“The only thing interfering with more widespread use is insurance payment,” she said.
Proponents of whole-genome sequencing, which has been commercially available for about six years, say it can help sick infants with potentially rare diseases avoid a months- or years-long odyssey of tests and hospitalizations without a clear diagnosis — and increase survival.
They also point to studies showing rapid whole-genome testing may lower overall health costs by reducing unnecessary hospitalizations, testing and care.
But the test may have its limits. While it is better at identifying rare disorders than older genetic tests, whole-genome sequencing detects a mutation only about half of the time — whether because the test misses something or the patient does not have a genetic disorder at all.
And the test raises ethical questions because it can also reveal that babies — and their parents — have genes that put them at increased risk for adult-onset conditions such as breast and ovarian cancer.
Even so, some doctors say sequencing offers the best chance to make a diagnosis when more routine testing doesn’t provide an answer. Pankaj Agrawal, chief of neonatology at the University of Miami Miller School of Medicine, said only about 10% of babies who could benefit from whole-genome sequencing are getting it.
“It is super frustrating to have sick babies and with no explanation what is causing their symptoms,” he said.
Some private insurers now cover the test with certain limitations, including UnitedHealthcare and Cigna, but others do not.
Even in states that have adopted the test, coverage varies. Florida will add the benefit to Medicaid later this year for patients up to age 20 who are in hospital intensive care units.
Florida state Rep. Adam Anderson, a Republican whose 4-year-old son died in 2019 after being diagnosed with Tay-Sachs disease, a rare genetic disorder, led the push for Medicaid to cover sequencing. The new state Medicaid benefit is named for his son, Andrew.
Anderson said persuading his GOP colleagues was challenging, given they typically oppose any increase in Medicaid spending.
“As soon as they heard the term ‘Medicaid mandate,’ they shut down,” he said. “As a state, we are fiscally conservative, and our Medicaid program is already a huge program as it is, and we want to see Medicaid smaller.”
Anderson said it took doctors more than a year to diagnose his son — an emotionally difficult time for the family as Andrew endured numerous tests and trips to specialists in several states.
“I know what it’s like to not get those answers as doctors try to figure out what is wrong, and without genetic testing it’s almost impossible,” he said.
A Florida House analysis estimated that if 5% of babies in the state’s neonatal intensive care units got the test each year, it would cost the Medicaid program about $3.3 million annually.
Florida’s legislative leaders were persuaded in part by a 2020 study called Project Baby Manatee, in which Nicklaus Children’s Hospital in Miami sequenced the genomes of 50 patients. As a result, 20 patients — about 40% — received a diagnosis, leading to changes in care for 19 of them.
The estimated savings exceeded $3.7 million — a nearly $2.9 million return on investment, after the cost of the tests, according to the final report.
“We have shown that we can justify this as a good investment,” said Parul Jayakar, director of the hospital’s Division of Clinical Genetics and Metabolism, who worked on the study.
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