Deadly diseases in Minnesota newborns to be targeted in new whole-genome study

MINNEAPOLIS – A federally funded study aims to determine if whole-genome sequencing at birth can reduce childhood diseases and deaths while satisfying growing concerns over genetic privacy and public health research.

Parents at two yet-to-be-selected health systems in Minnesota will be able to opt in to the BEACONS study and have their children’s genomes mapped out and analyzed for genetic defects that are associated with more than 700 treatable diseases.

Six states — Iowa, Minnesota, New York, Oregon, South Carolina and Texas — along with Puerto Rico were selected earlier this year for the trial. No child will be enrolled unless parents consent by opting in to the study.

Minnesota already has a screening program that analyzes the protein and chemical composition of blood samples from newborns (unless parents opt out) for more than 60 rare and hidden conditions, such as sickle cell disease, that can benefit from early diagnosis.

BEACONS goes further through whole-genome sequencing, which means mapping every gene in a person’s makeup and analyzing key mutations that are known to increase risks for specific diseases. The results are growing in importance because they can match patients to new gene therapies that slow or even reverse previously untreatable diseases, said David Largaespada, a professor of genetics and cell biology at the University of Minnesota.

“Biology doesn’t have to be destiny,” he said. “These devastating childhood diseases can be prevented, not simply managed.”

Collecting so much genetic information raises concerns, though, especially if it ends up in the hands of health insurance companies that could decide whether to deny benefits to people with certain genetic risks. A recent high-profile court case in New Jersey raised the question of whether police are illegally using genetic information collected at birth to look for criminal suspects.

A key goal of BEACONS is determining whether whole genome sequencing of newborns could be carried out in a way that addresses such concerns, said Amy Gaviglio, a genetic counselor and consultant who will lead a public advisory committee for the study. The researchers will be studying how different approaches to informed consent either encourage or discourage parents from signing up for the study, and following up with parents who decline to find out why.

“We are seeing very real and very understandable rising public scrutiny around consent, privacy and equity,” she said. “This is especially true in the post-pandemic era.”

Families in the BEACONS study will be able to request the genetic data they contribute, but it otherwise will be kept private and protected by a federal confidentiality certification. A contractor, GeneDX, will store the blood samples and genetic data for five years and then destroy them, unless parents ask for them to be destroyed sooner.

Gaviglio was part of an information session in St. Paul on Monday, April 6, to build public awareness in Minnesota about genetic testing and the upcoming three-year feasibility study. In addition to finding methods of consent that appeal to parents, the researchers hope to prove that universal screening of many newborns saves more lives than the current approach of testing a select few children after they begin to show symptoms of rare diseases.

While 99% of new parents consent to Minnesota’s existing state screening program, the number of opt-outs doubled from 206 in 2019 to 489 in 2024, according to state data. The increase coincides with an increase in parents refusing recommended vaccinations for their children.

Minnesota’s program also has faced court challenges from privacy advocates, who in 2011 won a Minnesota Supreme Court decision that ordered the state to destroy blood samples it had kept for future research and to validate its tests. State legislation three years later renewed Minnesota’s authority to collect and save that information, though.

Some parents consent to newborn screening when in the “fog of birth” and have misgivings later on, said Twila Brase, co-founder of the Citizens’ Council for Health Freedom, which led the legal challenge against Minnesota’s newborn screening program. She attended Monday’s session.

Infants have no say over the collection of so much genetic data that defines their entire lives, she added. “When you sequence a child at birth, you’ve sequenced the adult-to-be. That individual never gave consent, and they cannot get their genetic privacy back.”

The $27 million BEACONS study has a goal of testing 30,000 newborns across the U.S. Researchers in Massachusetts and Pennsylvania are leading the study, which is funded by both the federal government and two genetic testing companies, GeneDx and Illumina.

Three parents at Monday’s event spoke about how screening and diagnosis helped connect their children to treatments. Carolyn Philstrom teared up talking about her son, who was among the first in Minnesota screened for genetic risks of spinal muscular atrophy. His early diagnosis resulted in gene therapy and prevented the disabling symptoms that have affected other children.

“It was very scary at first,” she said. “He was completely healthy, had no signs or symptoms at all. The news at first felt like a crash, but from there the news kept getting better and better as we learned about the treatments available.”

Stacy Pike-Langenfeld lost her daughter at age 2 to Krabbe disease and has since become an advocate for parents of children with rare diseases that can be discovered through screening. She said there is a “death by ZIP code” problem in the U.S. right now because some families have access to screening and early treatment and others don’t.

Screening needs to focus on diseases that are treatable and the results need to be presented clearly to parents so they can make effective decisions for their children, she added.

BEACONS researchers decided to analyze the results only for about 700 genes linked to childhood diseases that have existing, federally approved treatments. Parents won’t be notified automatically about any genetic variations in their children that haven’t been definitely linked to inherited diseases. The study also won’t search for genetic variations linked to treatments that are currently experimental and available only through clinical trials.