SAN FRANCISCO (GenomeWeb) – As researchers and physicians struggle to figure out best practices for implementing genomics in the clinic, a number of integrated health systems have are making strides in using genomics for rare disease diagnosis, cancer testing, and even screening asymptomatic individuals to keep their populations healthy.
During a panel discussion at the Precision Medicine World Conference here this week, several clinicians talked about their progress and the benefits that come from implementing genomic programs within integrated health systems that serve as both provider and payor.
Geisinger, which recently launched a clinical version of its research project known as MyCode Community Health, that returns sequencing results for 76 actionable genes, has been at the forefront of moving genomics into the clinic. NorthShore University HealthSystem has also forged a number of partnerships with Ambry, Invitae, and Color Genomics, to bring genomic testing to its patients. Other health systems at following suit.
At PMWC, Cornelius Boerkoel, executive director for Sanford Health's Imagenetics Research Center on Genomics and Molecular Medicine, described Sanford's precision medicine program as "precision prevention" to distinguish it from standard clinical genetics clinics, which often focus on rare Mendelian diseases.
Sanford Health serves patients in the northern central states from around Minneapolis west through the Dakotas and into rural Oregon, Boerkoel said, and for about 30 percent of the patients Sanford is also the payor. The precision medicine program was launched in 2014 following a $125 million gift from philanthropist Denny Sanford.
Boerkoel said that Sanford's Imagenetics program decided to offer Illumina's Global Screening Array for SNP genotyping and to return results related to 59 medically actionable genes recommended by the American College of Medical Genetics and Genomics. It also offers pharmacogenomic testing. "The objective was to test 200,000 people and the health corporation wasn't up for running whole-genome sequencing on that many people," Boerkoel said.
One of the biggest challenges, Boerkoel said, was figuring out how to implement this type of screening within a primary care setting in a way that did not disrupt physicians, who wanted to provide higher quality care and understand the use of genomics in health but did not want to take time away from their practice to go back to school.
The health system first initiated online education program for the physicians and decided to embed genetic counselors at the major healthcare facilities so physicians would be able to consult them if needed. The health system also hired and trained pharmacists in pharmacogenomics. After completing the education step, the physicians were all given the option of being tested so that they could experience having results returned and the counseling that went along with that.
Sanford initially rolled out a pilot of the program to individuals who had enrolled in the biobank. Uptake among those individuals was between 40 and  50 percent, Boerkoel said, but when Sanford rolled the program out more broadly, uptake was only about 2 percent.
"That was disheartening," he said, but noted that the way the program was launched may not have been optimal. The program itself was not advertised and instead individuals just received an email saying that it was available. If the person indicated interest, that would set off a series of additional online surveys and educational videos the individual would have to get through before triggering an order for a blood draw. Boerkoel said that the researchers are now studying whether involving a physician more directly or doing more marketing of the program will increase enrollment.
Amy Compton-Phillips, executive vice president and chief clinical officer for Providence Health & Services, said that the health system, which has a network that extends from Santa Monica, California to Alaska and as far east as Montana, is "trying to deconstruct healthcare." Following research from the Institute of Systems Biology, which is now an affiliate of Providence, in which asymptomatic individuals had whole-genome sequencing, microbiome, metabolite, and proteomic testing, and also submitted data from wearable fitness trackers, Providence aimed to offer similar testing to its patients.
The study generated "rich data" and found that when paired with health coaching, outcomes were improved, Compton-Phillips said. So, the health system initiated a pilot with 1,000 of its employees. She said that it is currently in year two of a three-year study with two main goals: to see whether it can lower overall healthcare costs and improve patient outcomes.
The genomic, metabolomics, and fitness tracking data is combined with health coaching, she said, and early results have showed that "virtually everyone who participates is engaged with their healthcare."
Outside the US, similar healthcare systems have also begun implementing precision medicine programs. At PMWC, Varda Shalev, who heads the Morris Kahn and Maccabi Research & Innovation Institute in Tel Aviv, Israel, discussed Maccabi's plans to build a biobank and harness its extensive electronic medical record database, which contains longitudinal data on 2.5 million patients. It has already consented 60,000 individuals for the biobank and plans to collect samples periodically. It is also launching some disease-focused projects, including a sequencing study for Parkinson's disease and one for fatty liver disease.
Shalev said that being a large integrated health system is an advantage for such large-scale projects since its patients stay within the health system, providing both the opportunity to collect longitudinal data and the right incentives to both optimize healthcare and reduce costs.
Like Compton-Phillips and Boerkoel, she said the goal is to "change the way we practice medicine" in order to get better outcomes. She noted that there is a significant amount of waste in healthcare giving people drugs that they do not respond to or performing invasive screening procedures such as colonoscopies just because they've reached a certain age. Instead, she envisions being able to use genomic data to help make better decisions and improve outcomes.
Last month, Israel announced its plans to sequence more than 100,000 patients' genomes by 2023 and collaborate with Maccabi to use the tissue biobank.
While integrating genomics within these types of large healthcare systems has a number of advantages, there are still challenges for everyone looking to implement clinical sequencing programs.
As Boerkoel noted, there is an education gap — primary care physicians often have not been trained in genetics and don't understand quite how to use the tests. In addition, Compton-Phillips said that more clinical utility studies need to be done to prove that such programs really are cost-effective and improve health. Shalev added that as sequencing is used more proactively, determining when in an individual's life to sequence their genome and when and how to return results would be particularly challenging when considering children. "How do you do consent for that? And will such information help them or hurt them?" she said.