Pioneering studies show promise in sequencing a baby’s genome at birth
RALEIGH, N.C. - Tiffany King had given birth to her daughter, Fern, a little more than a month earlier and was back at her job as a construction manager when the phone rang. The caller said she had news about the infant’s genome, the complex genetic code found in virtually every human cell.
“Oh, no,” Tiffany said she remembers thinking. “That can’t be great.”
Researchers working on a study in North Carolina had discovered that Fern was born with a mutation in one of her 20,000 or so genes, a potentially harmful change linked to a condition called Pendred syndrome, the caller explained. The condition, which affects 2 to 3 of every 1,000 children, usually causes hearing loss, but sometimes also thyroid and balance problems.
Although Tiffany had hoped her baby would receive an “all clear” on the medical tests, she got over her initial anxiety.
“I’m a fan of having more information. Knowledge is power,” she said. “And as it turned out for us, that was very much the case.”
Born last November, Fern had blood drawn from her heel for North Carolina’s mandatory newborn screening, which tested for more than 60 medical conditions. Nothing was found. That could have been the end of the story. Instead, Tiffany and her husband, Matthew Vogt, a physician and scientist in Durham, decided to take the state up on a groundbreaking offer.
Free of charge, parents can have experts conduct a more extensive scan and review their baby’s entire genetic blueprint for 200 different conditions. One is Pendred syndrome, a condition not covered by the standard, more limited newborn screening.
North Carolina and New York are studying whether this far more comprehensive approach can save lives and improve children’s health. Two decades after scientists sequenced the first human genome, the two state studies reflect the rapid emergence of a new kind of health care called genomic medicine, spawned by that landmark achievement.
Early results show that genome sequencing is identifying conditions not disclosed through the traditional newborn screening required by all 50 states. Since North Carolina began its study in September 2023, the state has examined the genomes of more than 1,800 babies; 40 were deemed likely to have medical conditions that were not previously diagnosed. One newborn was flagged as likely to have two previously undiagnosed conditions.
“Some of those were for potentially life-threatening conditions,” said Holly Peay, lead investigator for North Carolina’s Early Check program.
Since launching its GUARDIAN program in September 2022, New York has sequenced the genomes of more than 10,000 babies; 299 tested positive for one of the 450 conditions the state has focused on.
“For one child, it was even lifesaving,” said Wendy Chung, head of pediatrics at Boston Children’s Hospital, who is leading New York’s study.
Existing newborn screening programs, which vary state to state and are credited with saving or improving the lives of about 12,000 babies a year, are expected to continue for the foreseeable future, experts said.
But dramatic changes during the last 15 years in the costs and methods of sequencing all of a patient’s genes, coupled with the promising early results in New York and North Carolina, suggest the technology may someday augment traditional newborn tests.
Most of the early sequencing cases, usually attempts to diagnose mysterious illnesses, scanned just a fraction of each gene ― the 1 percent known to contain the instructions for making proteins. Proteins are responsible for virtually every human action from breathing to thinking, and mistakes in proteins play roles in numerous illnesses, including Parkinson’s, Alzheimer’s, Type 2 diabetes and cystic fibrosis.
In the last two decades, the cost of reading the entire genome, not just the protein-coding parts, has plunged from more than $10 million a patient to about $1,000. Today, the cost is akin to that of routine medical tests, such as colonoscopies and MRI scans.
The technology marks a fundamental change in the way diseases are diagnosed, said Erica Sanford Kobayashi, a pediatric critical care doctor at Children’s Hospital of Orange County in California. The traditional way of diagnosing children, she said, “is that we see a problem and then we look for the gene that causes that problem.”
Sequencing reverses the process, allowing doctors to identify problems in a child’s genes before they trigger symptoms.
That was the case for Fern and for another baby born that same month at a hospital across the state near Charlotte.
Kristin and Jay Stark went through fertility treatment for seven years. The embryo they chose underwent genetic testing. Then, when their son, Landon, was born, his screening detected no health problems.
So when the opportunity arose to have North Carolina sequence their baby’s full genome they agreed. “It can never hurt,” Jay said, “It’s free. Better safe than sorry.”
Several weeks after their decision, Kristin was home getting ready for the day when she, too, got a phone call about her son’s genetic blueprint. Landon was born with a mutation that put him at higher risk of developing a rare condition called Alport syndrome, which affects about 1 in every 5,000 to 10,000 people, causing kidney disease, hearing loss and eye abnormalities.
The fertility and newborn screening tests had not searched for Alport syndrome.
“I personally felt like it was my fault,” Kristin said. “It was something I would have passed to him.”
“It’s not something you did,” Jay assured her. “It’s just something that happened.”
And although the news was a surprise, Jay felt prepared for the road ahead. He’d cared for his father, who had kidney failure and died at age 69 when his kidneys were compromised by covid-19.
“I knew there were dietary restrictions and medication restrictions” that patients with kidney disease must observe, Jay said. He was grateful to know about his son’s risk of developing Alport syndrome, because “there are things you can do to preserve life,” he said. “It’s not a death sentence.”
Landon now has his kidney function checked every six months. So far, he has not shown symptoms of Alport, and there is a chance he won’t despite the genetic mutation, Jay said.
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Getting ahead of genetic diseases
Fern’s parents, Matthew and Tiffany, also went through fertility treatment. Genetic tests had revealed that Matthew had a mutation linked to Pendred syndrome, though he had no symptoms. That made him a carrier for the condition.
At the time of the fertility examination, he’d looked up information on the syndrome. He figured it was unlikely his daughter would get it and “didn’t think much more about it.” His confidence seemed justified when Fern was born and passed her initial hearing test.
Then came the results of Fern’s genome, confirmed through a test involving a cheek swab.
Her parents adjusted quickly to the news. The reason they’d decided to have Fern’s genome screened, Tiffany said, was to “get ahead of it” if the baby had a condition.
They took her to an audiologist for a new hearing exam. This time, Fern showed a little hearing loss in the higher registers, and her left ear was a little worse than the right.
She now visits a hearing specialist every two to four months. Already, Tiffany is learning American Sign Language.
“If [Fern] needs a hearing aid, we’ll get her a hearing aid,” Matthew said. “If she needs a cochlear implant, we’ll get her one.”
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Ethics of early sequencing
Beyond its medical implications, sequencing a baby’s genome raises ethical concerns, which the parents and scientists in the study have had to weigh.
“There are a lot of ethical questions around what will be done with the information. Do insurance companies have access to it?” said Fern’s father, Matthew, the physician-scientist. The question, he said, is important “in this insane health-care system, where private companies have so much power to decide what happens. And I say that as a health-care provider and a father.”
North Carolina pledges it will not provide anyone outside the study with the names or contact information of participating babies or parents unless the family grants permission. New York promises that a baby’s screening results can be accessed only “by the people working on the study and the doctors caring for your baby.”
Among the most challenging issues raised by sequencing newborns: whether parents should be informed of mutations linked to incurable diseases that do not begin until adulthood. For now, North Carolina does not inform parents of such a finding, reasoning it should be up to the person with the mutation to make that decision when they reach adulthood.
The state is allowing parents to choose whether they wish to know their child’s risk for Type 1 diabetes, an illness that is treatable. Parents are also given the option of learning about mutations linked to more than two dozen rare diseases that are not currently treatable but have treatments under investigation.
Despite the plummeting costs of genome sequencing, there would probably be financial concerns about adopting the $1,000 test as policy for North Carolina, which records about 120,000 births per year. To date, the cost of North Carolina’s Early Check study has not been made public, said Peay.
However, some studies of genome sequencing have found that the technology can result in financial savings in the long run, especially when used to diagnose children sent to the neonatal or pediatric intensive care units with unknown diseases.
In California, a 23-month pilot study called Project Baby Bear examined use of rapid genome sequencing for critically ill babies covered by Medicaid. The technology helped to diagnose 76 of the 178 babies sequenced in the study, resulting in treatment changes for 55 babies. The rapid diagnoses, generally done in less than two weeks, also allowed doctors to discharge babies sooner.
The result: a total of 513 fewer days spent in the hospital, 11 fewer major surgeries and an overall health-care savings of more than $2.5 million.
In 2022, researchers performed an economic analysis of 38 critically ill children who had received rapid whole-genome sequencing. Scanning the genomes of all the children and their families cost almost $240,000. But the genetic information led to diagnoses for 17 of the children and reduced spending on pediatric intensive care by an estimated $185,000, according to the study, which appeared in the journal Frontiers in Pediatrics.
Sometimes, children are not the only ones to benefit from having their genomes sequenced. Often, when doctors identify a mutation in a child, they check to see whether the mom or dad has it.
Sanford-Kobayashi at Children’s Hospital of Orange County said in two cases, sequencing led not only to a child being placed on heart drugs called beta blockers, but to the child’s mother being placed on the same class of drugs.
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A lifetime of benefits?
One unknown is the medical value a child’s genome will have at different stages of life, a question under investigation by Jonathan Berg, a professor of genetics and medicine, and Laura Milko, assistant professor of genetics, both at the UNC School of Medicine in North Carolina. In about 15 months, they hope to launch a pilot study intended to form a bridge between newborn screening and adult screening.
Their study recognizes that although genetic conditions can be detected soon after birth, some won’t emerge for years. That puts parents in the position of having to keep schedules of different health measures they need to address when their child turns 2 or 5 or 10 years old.
Berg’s idea is to target different groups of genes at different times of life, allowing doctors to look for conditions when appropriate. If symptoms don’t begin until a child is 5 and cannot be treated before then, why identify it years before anything can be done?
“What we’re trying to balance,” Berg said, “is identifying the right information for the right person at the right time.”
Berg envisions a day when sequencing will help guide a patient’s care from infancy into adolescence and adulthood.
“I think we’ll be in this world where genetics is not just going to be, do it one time and be done with it,” Berg said. “We’re going to want to be doing genetic and genomic analysis all throughout life.”
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