At CHOP, ‘ultra-deep’ genetic testing detects rare mutations that cause debilitating childhood diseases

Dancing was medicine for Avery Rountree. Twirling, gracefully leaping, and raising her leg high above her head were among the few things that soothed her pain.

The teenager was born with malformed blood vessels and lymphatic ducts in her left leg, causing it to throb and swell with excess fluid. Medication didn’t seem to help much.

Wearing a compression stocking on her aching leg, she could compete like any other member of her team at DanceVibe studio in Mechanicsburg, Pa. But anytime she stopped moving — standing, sitting, even sleeping — she was in constant pain.

Then in April 2022, her physicians at Children’s Hospital of Philadelphia offered her hope. They had identified the rare mutation that caused her pain, using a new “ultra-deep” type of genetic testing far more powerful than traditional techniques. Developed in just the past three years, the technique is used in just a handful of medical centers around the world.

Her results, the Rountrees were surprised to learn, suggested she might benefit from a drug designed to treat a different disease, breast cancer.

Physicians at CHOP have now used this type of test to guide their choice of medication for 55 children with vascular anomalies, a collection of rare conditions in which any part of the body can become engulfed with painful, sometimes disfiguring overgrowths.

In some cases, the genetic tests prompted the doctors to start patients on a new drug. In others, the results suggested the children should stick with the medications they already were taking. So far, 35 of the 55 children have seen their symptoms improve, the team reported in a study in June, published in Nature Medicine.

In Avery’s case, the abnormal growths in her left leg were not cancerous, the doctors reassured the girl, then 13, and her parents. But the tests revealed that she carried a mutation that plays a role in some cancers. The breast-cancer drug might help.

But there were risks. The drug might not work. There could be side effects, including hair loss. And because she’d be part of a clinical trial, she might not even get the drug, but rather a placebo.

The young dancer was eager to try. Yet a few months into the trial, Avery’s pain got worse, to the point she could not dance at all.

At first, Avery’s condition seemed like no big deal.

She was born with purple splotches on her left leg, and her pediatrician said they were a type of birthmark that would probably disappear by the time she turned 5.

Instead, when she was 4, one of the spots turned a darker color, becoming puffy and tender to the touch. Her whole left calf started to swell, too, and it became painful to sit or stand.

Her mom, Tobie, took her to Dell Children’s Medical Center in Austin, Texas, where the family lived then, and learned that the girl’s condition was not going away. It was the first time they heard the words “vascular anomaly,” along with a slew of other medical terms, and Tobie Rountree was overwhelmed.

She called her husband from the car and said: “Never again am I going to the doctor by myself.”

The Rountrees soon became fluent in the jargon of their daughter’s condition, learning that disorders of the vascular system are as diverse as they are bewildering. One was called vanishing bone disease, in which the vessels that connect the lymph nodes grow out of control, eroding the patient’s bones to the breaking point. Other vascular anomalies can cause the arms or legs to swell to four times normal size. Still others cause lymphatic fluid to leak around the heart and lungs, making it difficult to breathe.

An MRI revealed unusual growth in Avery’s capillaries and some lymphatic vessels in her left leg. She underwent several rounds of treatment called sclerotherapy, which sometimes is used to treat varicose veins. A substance was injected into her abnormal blood vessels, causing them to become blocked with scar tissue.

But it was a temporary solution, as abnormal blood vessels would grow right back. If she sat down or stood still for any length of time, fluid pooled in her leg, and it was torture. Dance class, which she had started as a 3-year-old, was the only thing that brought her real relief, whether from the boost to her circulation or the joy of doing something she loved.

“It’s a distraction,” she said.

The family moved to Pennsylvania when Avery turned 9, and one of her Texas physicians gave them this parting message:

If you’re moving anywhere close to Philadelphia, you need to take Avery to CHOP.

Two decades after scientists deciphered the complete human genome, DNA testing now seems almost commonplace. Amateur genealogists use test results to find long-lost relatives or explore their heritage. Police use them to solve cold cases. And increasingly, physicians use genetic testing to select treatments for their patients.

But with conditions like Avery’s, it can be a challenge, said Denise M. Adams, director of the Comprehensive Vascular Anomalies Program at CHOP.

That’s because these conditions are generally not inherited, instead resulting from a mutation that occurs during pregnancy. That means the mutation is present in a small number of cells, not throughout the body, so it can’t be detected with a cheek swab or a drop of saliva.

“It’s not like Ancestry.com,” she said.

Doctors sometimes try to identify a telltale mutation by taking a biopsy from the affected part of the child’s body, she said, but that doesn’t always work.

Instead, the geneticists at CHOP perform what they call “ultra-deep” genetic sequencing, identifying minute amounts of mutated DNA floating freely in the child’s blood or lymphatic fluid.

This mutated DNA is present in a small fraction of the blood, so in order to find it, geneticists must amplify the sampled genetic material by thousands of times, said Hakon Hakonarson, director of CHOP’s Center for Applied Genomics. The team then uses sensitive tools to pinpoint the location of the mutation.

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Avery was eager to try it. She was already taking one medication that had helped some children with conditions similar to hers, called KT syndrome, but it didn’t seem to have much of an effect. The swelling in her leg had gone down somewhat, but the pain was just as bad as before.

The genetic tests revealed she had a mutation in a gene called PIK3CA. Adams told the Rountrees that a different drug called alpelisib — the one that had been approved to treat breast cancer — might help.

Avery would be eligible to join a Novartis-sponsored trial of the drug.

Her parents were reluctant. The drug might cause side effects, including headaches, fatigue, and hair loss. Then there was the chance that their daughter didn’t even get the drug. One-third of trial participants would start on a placebo.

But the young dancer had no qualms.

“Avery was adamant,” her mom said. “She wanted to try this both for herself and for others.”

In July 2022, she took her first pill.

By late October, it was clear that whatever Avery was taking had not worked.

Her pain had become so excruciating that she couldn’t dance. She stayed on the sidelines while her teammates practiced their moves, taking notes to memorize the choreography.

Eventually, Avery’s leg hurt so much that she had to stay home from school.

Her physician urged her to consider withdrawing from the trial and going back to the old drug, which seemed at least to have kept her stable.

No way, Avery replied. Even if she was among the trial participants on a placebo, she knew that in the 17th week of the trial, all participants were being switched to the real medication. It was Week 15. If she could just hold out for two more weeks…

Her mom supported her choice. An elementary school teacher, Tobie Rountree believed in letting adolescent children learn to advocate for themselves. She told her daughter’s physician:

“She’s 13.5 years old. If she thinks she can do it, we need to listen to her.”

Avery went back to school, and she kept taking the daily pill, which her mom now suspects was the placebo. And in November, the teenager started on a daily dose of 50 milligrams of the experimental drug, later increased to 125 milligrams.

Nothing happened at first. Then, little by little, the swelling her leg receded.

And eventually, she felt well enough to dance.

“It has been a very difficult year,” she said. “I feel like I’ve definitely come a long way.”

A full assessment of how well the drug works in Avery and the other children will come in several years, after statisticians carefully analyze all the scans and lab results.

For now, the Rountrees have no doubt — despite a setback at the end of April.

Avery was getting ready for the last big dance competition of the season, putting in 15 hours of weekly practice at the studio, when she suffered a painful blood clot in her left leg. The family got on the phone with Adams, their physician at CHOP. Was she OK to dance?

Adams left it up to her patient.

In the solo portion of the competition, Avery came in third place. It was the highest she’d placed all season.