By Monica Heger
The Mayo Clinic's Center for Individualized Medicine is launching a number of programs designed to bring whole-genome sequencing into the clinic and plans to outsource much of its sequencing to Complete Genomics to help supplement its in-house capabilities.
Among the clinical sequencing projects it is launching is a study to sequence breast cancer patients who require neoadjuvant therapy and surgery, in order to guide second-line treatment. The clinic will also conduct a whole-genome sequencing study to figure out how best to return results to patients and a pharmacogenomic study that will supplement patient medical records with sequence data on a select number of genes related to drug response.
Finally, Mayo researchers are developing targeted sequencing-based diagnostic tests for hereditary colon cancer (CSN 5/10/2011) and mitochondrial diseases.
Gianrico Farrugia, who heads Mayo's Center for Individualized Medicine, told Clinical Sequencing News that the goal of these projects is to "find out what will make a clinical difference" and integrate sequencing in a "very logical, testable fashion."
The Mayo Clinic has a "model of care that involves an inherent encounter with patients and technology to deliver medicine," and "we now think that genomics has a place to play, so we want to begin to incorporate this knowledge in our day-to-day practices," he added.
While the Mayo has in-house sequencing capabilities through its Medical Genome Facility, which runs the Illumina HiSeq and the Pacific Biosciences RS, it recently struck an agreement with Complete Genomics to provide whole-genome sequencing services to supplement its own capacity.
Farrugia said that Mayo's in-house Illumina machines are currently doing the majority of the sequencing work for the center's programs, but the Complete Genomics deal will give researchers another option. It has "no tie to one particular study," but will instead be a "resource for Mayo investigators in general," he said.
Breast Cancer Trial
Farrugia said that the Mayo team plans to start enrolling breast cancer patients to the sequencing trial within the next few weeks. The trial is not restricted to any particular subtype of cancer, he said, but only patients seen at the Mayo Clinic that require surgery and need neoadjuvant therapy will be eligible.
The trial will last around two years and 100 patients each year will be enrolled.
Sequencing will occur at two stages: after a biopsy but before a patient has been started on therapy, and then again after an initial round of neoadjuvant therapy and surgery.
Farrugia said that the team will likely begin with exome sequencing, but move to whole-genome sequencing as the cost drops.
A team of experts will discuss the sequencing results and determine which should be returned to the patient's oncologist. They will return results for which there's both data in the literature suggesting that the gene or gene pathway has an impact on disease and also for which there is a therapy that hits that target, Farrugia said. "Both need to be fulfilled to have in the clinical setting an actionable result," he said.
Results that are returned will first be validated with Sanger sequencing.
The goal of the trial is to test whether sequencing can identify a second-line of treatment, if needed, for patients.
Returning Sequence Results
Another project will seek to develop standards of practice for returning sequence information to patients. In this project, Mayo researchers are sequencing the whole genomes of biobanked samples from patients who consented to the research but have since passed away.
Farrugia said that this helps avoid the issue of what to do if disease-relevant variants are found in those samples.
"We're using it as a learning experience," he said. "It's a theoretical exercise." The team will go through all the steps of sequencing the samples, analyzing the data, and figuring out how the data would be shared. This will help them test the procedures and work out any kinks before implementing it on actual patients.
"We can run the trial, model it, and come up with all the things we would not have predicted, and then deal with them in a safe manner," Farrugia said.
The team is currently starting with 40 patients and may scale up from there.
Another project will address not only how to return sequence data to patients, but how to integrate genomic data into patient medical records. That study involves sequencing a limited set of so-called "pharmacogenomic genes" that are associated with drug response.
Mayo researchers plan to develop a targeted sequencing assay for 83 pharmacogenomic genes in collaboration with researchers at the National Institutes of Health. The team will start with a pilot of 1,000 patients at the Mayo Clinic and will incorporate that data into the patients' medical records.
The goal is figure out how to link the data to the medical records in such a way that if a patient is prescribed a drug that will cause an adverse response, it will trigger an alert to the physician prescribing the drug.
The 1,000-person pilot will also serve as a model to "figure out how to do it for all patients at the Mayo Clinic," said Farrugia. This project will likely kick off in the second half of the year.
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