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Started by Center for Individualized Medicine (@samuelsmith5209) · Thu, May 1 at 12:42pm CDT

Sharing Experience and Gearing Up for Expansion

Article Originally Featured on Genome Web

Mayo Clinic representatives reflected on the strategies used to establish the Mayo's standalone Individualized Medicine Clinic in a new publication, as the center gears up to offer clinical whole-exome sequencing for a broader set of conditions.

In an article published online in the American Journal of Medical Genetics' Seminars in Medical Genetics in mid-March, the team touched on the rationale behind the clinic's creation and oversight. It also offered a look back at individualized medicine experiences and outcomes at the Mayo Clinic center so far.

For instance, although the study's authors noted that the investment needed to establish the IM Clinic was comparable to that of designing and outfitting a new department, they argued that the single, shared personalized medicine center offers advantages related to everything from the speed of testing to the interpretation of patients' genomic data.

"Our approach was that we needed to have relevant infrastructure to do it all," corresponding author Gianrico Farrugia, a gastroenterologist and director of the Mayo Clinic's Center for Individualized Medicine, told Clinical Sequencing News.

The Center for Individualized Medicine, or CIM, was established in 2012 following a Mayo Clinic decision to focus more extensively on regenerative medicine, high-value healthcare delivery, and personalized medicine.

"We're very willing to share our mistakes so that you don't have to repeat them," Farrugia said.

The CIM is run by a group of representatives from Mayo Clinic sties across the US, Farrugia explained, and has been tasked with both personalized medicine research and translation related to the microbiome, biomarker discovery, epigenomics, pharmacogenomics, and clinical application of omics technology.

Those programs, in turn, are supported by corresponding infrastructure programs — from a biorepository to house appropriate samples to infrastructure related to sequencing, bioinformatics, and bioethics.

On the clinical translation side, meanwhile, the CIM spawned a new, multidisciplinary center known as the Individualized Medicine Clinic, which houses its own administrative staff, medical geneticists, oncologists, bioinformaticists, bioethicists, genetic counselors, and so on. As such, the Mayo Clinic's foray into personalized medicine involved investment in not only biorepository and sequencing-related infrastructure but also in related staff, including dozens of bioinformaticians, information technology staff, members of a bioethics team, and genomic counselors.

The clinic is offered at Mayo Clinic sites in Rochester, Minn., Jacksonville, Fla., and Scottsdale, Ariz., and is managed by a single board that meets regularly by video conference to discuss and approve cases at each locale.

Since opening its doors in late September 2012, the IM Clinic has focused on using genomics to look for disease-relevant genetic glitches in individuals with advanced cancer and those dealing with apparent genetic conditions that have not yet been diagnosed.

Those patient groups were specifically selected because they appeared most apt to benefit from whole-exome sequencing right away, Farrugia explained, though there are many other areas where genomic medicine is expected to prove useful in the future.

Indeed, the IM Clinic is gearing up to introduce additional testing areas later this year, he said.

"At some point in Q2 or Q3, we'll add items for patients who are interested in knowing more about heritable diseases, some pharmacogenomic gene panels, and certain disease panels."

The center is also coming up with a plan for applying whole-genome sequencing in clinical programs available at the IM Clinic. The timeline for introducing that type of genetic test is still being evaluated, though clinical trials are underway on individuals with cardiology conditions and cancer to guide the clinical implementation of whole-genome sequencing and transcriptome sequencing.

Findings from such trials are expected to inform the type of clinical sequencing tests offered at the IM Clinic in the future, Farrugia noted.

For their recent article in AJMG, he and his co-authors focused on experiences applying array comparative genomic hybridization, gene panel sequencing, and/or whole-exome sequencing in the first two patient groups considered through the IM Clinic, namely those with advanced cancers and "diagnostic odysseys."

Roughly 150 patients went through the Individualized Medicine Clinic in the first year after it opened. The center is now on target to serve hundreds of individuals per year, according to Farrugia, who noted that patients can either be referred to the clinic by their physician or visit it directly.

So far the team has tracked down clinically informative genetic alterations in around 30 percent of the diagnostic odyssey patients tested through the IM Clinic. The proportion of advanced cancer cases in which clinically actionable alterations have been detected is much higher, with targetable genes turning up in the majority of patients, though Farrugia explained that it's often still difficult to define successful clinical outcomes in that patient group.

There have been a number of tweaks to the methods being used to acquire, test, and interpret patient DNA patterns since the center opened just over a year and a half ago — from the methods used to collect and process samples to tweaks in the format for returning results to patients.

"There are things we're learning on the way and we'll be sharing them over time," Farrugia said.

He noted that the availability of genomic testing services offers an option for centers interested in delving into personalized medicine without investing heavily in related staffing and infrastructure.

"You can do this relatively cheaply, for example, if you decide to offer it and to send out Foundation Medicine panels and rely on that report," he said. "You don't need to have any storage and you can do it relatively cheaply."

For their part, the CIM members behind the IM Clinic opted to establish an independent center capable of carrying out each stage of the patient counseling, sample preparation, sequencing, and analysis pipeline, if necessary.

Nevertheless, the clinic relies on a range of testing sources, including gene panels developed at the Mayo Clinic, those offered by Foundation Medicine, and sequencing from the Baylor College of Medicine's sequencing center.

The IM Clinic mainly uses Illumina instruments for its in-house sequencing but is keen to "aggressively" expand it sequencing capacity in the future, Farrugia said.

There are also plans to add at least half a dozen new drug-gene interactions to the Mayo Clinic developed algorithm currently used to assess possible drug treatments in relation to patients' genotypes.

Earlier this year, researchers at the Mayo Clinic outlined efforts to fold pharmacogenomic data into patients' electronic medical records as part of a collaboration between the CIM, the Pharmacogenomic Research Network, and the Electronic Medical Records and Genomics Network.

The actual price of attaining whole-exome sequences varies depending on whether the sequencing is done in house, at Baylor, or elsewhere, according to Farrugia, who said that the exact cost of those tests remains proprietary.

Even so, those involved with the center have taken steps to keep the cost to patients relatively constant, so that the sequencing services offered at the IM Clinic are equally accessible to all individuals who may benefit from them.

The process of attaining insurance reimbursement for patients treated through the Mayo's IM Clinic is still evolving, given the relative novelty of such tests. Still, Farrugia said he's been somewhat surprised at the level of reimbursement that's been attained by the center's patients so far.

"We've found that if the rationale for doing it is well thought out, we're finding a reasonable insurance reimbursement — in fact, more than we expected," he noted.

In parallel with clinical sequencing and research efforts, the CIM is offering a formal training and education program for physicians seeking accreditation to be part of the IM Clinic. The center also has an education infrastructure program designed to educate physicians, nurses, pharmacists, and other healthcare providers who interact with patients entering the IM Clinic, and it includes an education component in its annual individualized medicine conference each October.

Despite some of the remaining challenges associated with applying genomics in the clinic, Farrugia argued that the individualized approach holds value for patients and is worth pursuing by institutions still on the fence with respect to its implementation. He recommends that such centers reach out to those with experience in the field to avoid duplicating trouble-shooting efforts already done at the IM Clinic and other sites already offering clinical sequencing.

"We're very willing to share our mistakes so that you don't have to repeat them," Farrugia said.

 

 

 

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