At the New York Genome Center, says Vaidehi Jobanputra, PhD, vice president and chief of clinical genomics, the laboratory is not directly involved in deciding who needs testing; at most of the hospitals they serve the decisions are made by clinical geneticists and neonatologists. When questions arise about results, the lab’s genetic counselor on staff, as well as Dr. Jobanputra, Dr. Guha, and other board-certified molecular geneticists, are available for discussion. “This multidisciplinary discussion is important—we help them understand the report,” says Dr. Jobanputra, who is also professor of pathology and cell biology, Columbia University Irving Medical Center.
That approach grew out of their first NICU study using rapid genome sequencing, focusing on patients with congenital heart disease. Though it involved a small number of patients, says Dr. Guha, “We were establishing the pipeline, and how to report, how best to serve the patient.” Pathogenic and likely pathogenic variants were, for the most part, fairly straightforward to explain to physicians and patients. But even then, the results didn’t always explain the entire phenotype. And when variants of uncertain significance were added to the mix, results became even more complex. In a field where everyone is spoiled for choice, “There can be a lot to explain,” says Dr. Guha, who also is a member of the CAP/ACMG Biochemical & Molecular Genetics Committee.
The Minnesota laboratory validated whole exome sequencing in 2017, and in 2021 it validated whole genome sequencing.
The following year, Bower says, the lab began to work more closely with NICU clinicians to offer whole genome sequencing for patients who were likely to benefit from such testing, including those born with what looked very suspicious for a genetic condition, and those with multiple, complex health problems with no specific suspicion for a condition, but where the clinicians were trying to rule in or rule out an underlying genetic component.
The need to return results quickly has always been paramount. While the NY Genome Center is licensed in all 50 states, says Dr. Jobanputra, the need for rapid turnaround times for this patient population means the center currently performs NICU rapid genome sequencing only at New York City hospitals. How rapid is rapid? “That’s a tough one,” she says with a laugh. “Rapid is a range. For some testing that means one day. But five to seven days is what we call rapid.”
In Minnesota the clock-watching has recently become even more urgent. In 2025, a new state law mandated insurance coverage for rapid genome sequencing in critically ill pediatric patients, including those in the NICU. The requirement calls for results to be finalized within 14 days, says Bower, who adds, “They’re a little vague on what point starts the clock.”
It’s not necessarily hard to get results to clinicians quickly if there’s an obvious, clear answer to the question they’re asking, Bower says. But that’s not always the case. And meeting the new state law requirement can be challenging in other ways.
“One is when you’re a smaller operation like ours, where we only do testing for people in our institution,” says Bower. “Batching is always a concern—you can’t just pull a technologist off another bench or run the sequencer every time a sample comes in.”
Behind these impediments lies another one, Bower says. He and his colleagues often do deep analytical dives as part of the testing, he says, with plenty of back and forth between the lab and clinicians, and sometimes procuring samples from family members. That takes time, and as time dwindles, they might have to reconsider how detailed they need to be.
As Bower notes, “Easy and clear genetic answers are not often that hard to find. So you could modify the scope to find slam-dunk answers that an off-the-shelf box to bioinformatic solution can get.” That might also make the testing more affordable, though such an approach might overlook unusual, possibly relevant variants.
“I think our inherent bias is we always want to get an A+ and do our best effort,” Bower says. But to provide more equitable care, might it be acceptable to do “B” work? “Which is still really good, and it gets the easy things in a more affordable way,” he concedes.