SAN FRANCISCO (GenomeWeb) – Geisinger Health System said this week that it plans to start rolling out clinical exome sequencing to its patients, starting with an initial 1,000-person pilot that will return a limited number of medically actionable results to patients.
The pilot builds off Geisinger's ongoing research project, the MyCode Community Health Initiative, in which individuals who consent to research can get their exomes sequenced and obtain results from 76 medically actionable genes.
The project originally started in 2007 as a biobank, but expanded to include exome sequencing when Geisinger partnered with Regeneron Pharmaceuticals in 2013 to perform the sequencing. Around 200,000 patients have enrolled in the MyCode initiative so far, and as of May, almost 93,000 exomes had been sequenced and 552 participants received results indicating that they have disease-causing variants.
During a conference call with reporters today, David Feinberg, Geisinger's president and CEO, said that Geisinger plans to continue its research protocol but will also begin to start offering sequencing to patients "as part of routine care" at "no cost."
Geisinger is an integrated health system that includes a hospital system, a physician network, and insurance. About half of the business is integrated, Feinberg said, meaning patients have Geisinger insurance and receive care from Geisinger doctors at Geisinger hospitals. Testing will be available for patients regardless of whether the patient is insured by Geisinger or another payor, Feinberg said.
David Ledbetter, Geisinger's chief scientific officer, said during the call that the Geisinger team has been "especially pleased by the very positive response by our patients and primary care physicians" to the MyCode research study. Patients who have undergone sequencing have started to realize the benefits of identifying risk variants. For instance, at a conference in January, Ledbetter described one patient for whom MyCode identified a BRCA1 mutation. The woman had no family history, but opted for prophylactic surgery to remove her breasts and ovaries because she was raising grandchildren. Upon surgery, the doctors discovered a tumor, were able to remove it, and the patient is now doing fine.
The "genomics team is excited to transition from this research framework and start clinical pilot projects, on a small scale initially, but [to] rapidly learn how to scale this to make it available to all patients," he added.
Feinberg said that the clinical exome sequencing test would be offered for free to patients, and he estimated its cost at $500 per test. Geisinger would cover the cost through a mix of internal funding and donations it has received.
Any follow-up appointments or testing would be covered according to patients' healthcare plans. For instance, he said, if a patient's exome test identified a pathogenic BRCA mutation, follow-up appointments with a doctor would be covered depending on the specifics of the healthcare plan, with patients responsible for copays associated with doctor's visits or subsequent treatment.
One of Geisinger's main goals is to demonstrate that pre-emptive genomic testing is cost-effective. Feinberg said that through the MyCode project, the team has found that around one in 250 people have variants putting them at risk for familial hypercholesterolemia, a genetic disorder that causes individuals to be unable to metabolize cholesterol, leading to premature cardiovascular disease. Feinberg said that the disorder has a 50 percent morbidity rate by age 40 if not treated aggressively, and the American Academy of Pediatrics recommends that patients with the genetic defect should be started on medication by age 8. "Theoretically, if we find out all the people who have this gene and treat them appropriately, we'll save on costs," he said.
Similarly, he said, around 50 percent of women who have a BRCA mutation do not have a family history of breast or ovarian cancer, he said. By screening broadly, "we're going to find those people" and "can intervene."
"We believe we'll be able to show the economics of that by doing the testing," he said, although he noted that it would take time.
Geisinger is still working out a number of details for the clinical implementation, including which findings will be returned to the patient. As part of its research protocol, Geisinger returns results related to 76 genes, including the genes recommended by the American College of Medical Genetics and Genomics as being clinically actionable. Ledbetter said that Geisinger was still deciding whether to return findings related to the same list of genes or whether to report on a more limited number of genes. For instance, it is also considering reporting on just those genes that are deemed Tier 1 by the US Centers for Disease Control and Prevention — the BRCA genes, Lynch syndrome genes, and familial hypercholesterolemia genes.
 "We're still finalizing those decisions," Ledbetter said, "but it will be a list of strongly evidence-based single-gene disorders or dominant genetic disorders with high penetrance with clear medical interventions."
In a follow-up email, Ledbetter noted that Geisinger has also not decided where the clinical sequencing will be performed. Regeneron's sequencing facility is not currently CLIA certified, but he said Regeneron may seek certification in order to do Geisinger's clinical sequencing. Other solutions would be to set up clinical sequencing within Geisinger's own CLIA-certified laboratories or to outsource to another vendor, Ledbetter said.
In addition, the way in which patients are consented for testing will be slightly different compared to the MyCode study, Feinberg said. For the MyCode study, Geisinger has so-called consenters in physicians' waiting rooms, where patients who agree to enroll go through the consent process. They then schedule the follow-on blood draw for a later date. For the clinical version, physicians will discuss the test with their patients during the appointment — whether a routine check-up or a visit for an acute need. In that case, the patient is not signing a consent form, but agreeing to a lab test. All patients who sign up for clinical testing will receive a clinical report, even though the majority will be negative. By contrast, participants in the MyCode initiative only receive results when they are positive for disease-causing variants.
Ledbetter said earlier this year that Geisinger's ultimate long-term goal is to offer sequencing to all its patients at birth, to help guide healthcare. This clinical pilot will be a first step that will inform that future goal, he said.
"Most of the genetic conditions we are able to detect are adult-onset conditions with no medical actionability in children, so starting with adults is fine," he said. "As costs come down and we gain experience, screening children could have additional value in identification of childhood-onset conditions."