The Mayo Clinic and startup Silicon Valley Biosystems are joining forces to develop a clinical sequencing pipeline that Mayo plans to implement within its Center for Individualized Medicine for cancer patients and patients with rare, undiagnosed diseases.
The collaboration expands on plans the Mayo Clinic announced around a year ago to begin implementing sequencing as part of routine patient care (CSN 2/15/2012).
At the time, Gianrico Farrugia, who heads the Center for Individualized Medicine, told Clinical Sequencing News that the center had several different clinical sequencing initiatives, including developing targeted sequencing-based diagnostic tests for hereditary colon cancer and mitochondrial diseases, conducing a study to evaluate sequencing's ability to guide second-line treatment of breast cancer patients, and sequencing biobanked samples from diseased patients to figure out how best to return results to patients.
Farrugia told CSN recently that these efforts are ongoing. The center is preparing to launch its first certified targeted sequencing-based laboratory-developed test, although he declined to specify for what indication. In addition, he said that the breast cancer sequencing initiative is around a quarter of the way completed.
However, he said that the breast cancer trial and other clinical trials for which Mayo is performing sequencing are research oriented, while the goal of the Center for Individualized Medicine is to adopt sequencing in routine patient care.
As such, the Mayo has invested in the CLIA certified Clinical Genome Sequencing Laboratory, for which it has the Illumina HiSeq and MiSeq, as well as an Ion Torrent PGM. While the lab itself is CLIA certified, the clinical sequencing pipeline it is developing with SV Bio is not yet certified, although it expects to have the pipeline CLIA certified sometime this year.
SV Bio was founded about a year and a half ago by Dietrich Stephan, formerly chief scientific officer of the Cancer Genome Institute at Fox Chase Cancer Center, founder and CEO of the Ignite Inova Institute, and founder of direct-to-consumer genetic testing firm Navigenics.
The company, which has financial backing from Sequoia Capital, is offering genomic data interpretation services using a proprietary interpretation pipeline that identifies disease-causing genetic variants and provides this to health professionals along with relevant information from published literature about the mutations.
The Mayo collaboration with SV Bio is "focused more heavily on our patients in routine patient care," Farrugia said. In particular, the Center for Individualized Medicine focuses on two patient populations: those with cancer and those who have undergone diagnostic odysseys.
The center will initially begin with a clinical exome sequencing pipeline, but will eventually scale up to clinical whole-genome sequencing, Farrugia said.
For a patient to qualify for clinical sequencing, Mayo physicians must first request a consultation through the patient's electronic medical record.
"The consultation is triaged by a set of physicians that have been trained in the space, and they, along with an oversight board, make decisions about enrolling patients into the clinic, as well as interpret the data on the back end to help make care decisions," Scott Beck, the administrative director of the Center for Individualized Medicine, told CSN.
Beck said that SV Bio's pipeline will be installed both at the Mayo and also at SV Bio's offices in Foster City, Calif. "We'll be jointly developing the software based on what they're already bringing to the table in terms of the pipeline," he said. "As we're bringing patients through, generating data, analyzing it, and interpreting, we're also bringing a lot of medical expertise and perspective" to contribute to co-developing and improving the pipeline over time, he added.
Sequencing of the patients will be done at the Mayo Clinic and also at SV Bio.
Mayo currently runs the Illumina HiSeq and MiSeq and the Ion Torrent PGM out of its CLIA-certified sequencing lab, and will evaluate both platforms for its clinical sequencing pipeline. In addition, the clinic also has HiSeq systems, another MiSeq, and a Pacific Biosciences RS available for research purposes through its Medical Genome Facility, which primarily supports the clinic's research community and early-stage validation of next-gen sequencing-based tests for the clinical laboratory.
"We recognize the fast pace of change in the market," said Beck, "and like most other academic centers or teaching institutes, we want to make sure we're keeping our options open."
The center will also consider outsourcing some of its clinical sequencing work, as long as "Mayo's sequencing standards are met," he added.
The center last year struck up an agreement with Complete Genomics to outsource much of its sequencing to help supplement its in-house capabilities. Beck said that the center is still outsourcing to Complete as well as to Illumina for some of its research-related projects, "where it makes sense," like for whole-genome sequencing projects with large numbers of samples.