Within a newly created Institute for Precision Medicine, clinicians from Weill Cornell Medical College and New York Presbyterian Hospital plan to use whole-genome and exome sequencing, as well as other genomic and genetic analyses, to inform individualized treatment for cancer patients.
Moving forward, the center will also use genomic data to guide care for other disease areas, according to its leader, Mark Rubin, a professor of pathology at Weill Cornell.
Rubin said the institute is currently awaiting regulatory approval from CLIA and New York State. With that approval in hand, the institute will begin sequencing patients to inform more personalized treatment strategies — first focusing on cancer, and then eventually broadening to other disease areas.
While Rubin did not detail how the institute will recruit patients, he said the center plans to address both patients who can benefit from relatively simple molecular analysis, like single-gene tests, as well as those with advanced disease and no current treatment options and patients who stop responding to standard treatments and could be redirected to other therapies based on a discovered gene alteration.
According to Rubin, the institute plans to use sequencing, including whole-genome and exome sequencing, as a central tool to guide therapy decisions for this second group. But, he added that sequencing will not be an exclusive tool for the institute.
"For some patients, there are very clear indications of whether they need a specific targeted therapy. Those are pretty straightforward," Rubin said.
"It may turn out that the most efficient way to determine if someone has a certain mutation, like EGFR, is to run the single-gene test up front. That's not going to change for some types of disease … so what I see our role being is developing these more complex approaches," such as whole-genome sequencing or gene panels.
"There is emerging data that sequencing, either exome or whole-genome, can provide insight on which treatments cancer patients might need that are not considered standard treatments," he said.
Weill Cornell currently houses an Illumina HiSeq 2000 and MiSeq, but Rubin said the institute is planning to be agnostic in terms of what platforms it will use for genomic and genetic analysis in the future.
Rubin said that the institute is also developing a program for obtaining patients' consent for whole-genome or exome sequencing. The process will likely take a menu-style format, he said, based on a strategy developed by the University of Michigan.
"As part of consent, we would give patients some options, so either they have no wish to learn about the genomic information, or they want to learn just about actionable alterations, or they want to learn everything," he explained.
While the development of genomically targeted therapies is relatively accelerated in cancer compared to other disease areas, Rubin said the institute does plan to expand its approach to other populations, like cardiovascular and neurodegenerative disease, and possibly infectious disease.
In addition, he said the group is also discussing how it might use genomic information to look at disease risk, with the potential to inform early interventional treatment decision making.
"Because we are a hospital that sees [healthy] patients being followed by their doctors, that's something we're contemplating as pilot," he said.
"We don't have a plan in mind yet, but those types of studies are probably very important in specific disease entities, for patients at risk for a particular constitutional disease … or you could imagine we might screen large numbers of our patient population to look for risk factors that may not have been identified yet," he said.
Rubin said the institute plans to do its own in-house sequencing toward its central goal of guiding therapy for patients, but it also may work with the New York Genome Center on longer-term studies involving larger patient populations that don't require a rapid turnaround time, or with retrospective samples.
"In real time we would probably need to do [sequencing] in house so we can make sure we have a clinically relevant turnaround time," he said.
"But for larger retrospective studies, or studies with prospectively collected samples that maybe we analyze later, we could envision working closely with the New York Genome Center … That would be a way to facilitate larger trials to look at the information after patients have been initially treated.
"That might also be a good way to make sure we have the optimal tests or that we are using the best technology for what we are trying to do," he added.
While the Weill Cornell Institute forges ahead, several other academic centers are also exploring using whole-genome or exome sequencing to inform cancer care in the clinical setting.
Under a Clinical Sequencing Exploratory Research Program funded at the end of 2011, the National Human Genome Research Institute is supporting six centers in studies of how genome sequencing can best be used to guide care for patients with cancer and other diseases (CSN 12/7/2011).
Meanwhile, other academic and commercial groups are already offering whole-genome or whole-exome sequencing services that could potentially inform care for a variety of diseases, as well as targeted cancer sequencing tests to find selected actionable mutations. For example, Fox Chase Cancer Center announced last month that it has begun offering targeted sequencing to inform cancer treatment using an adaptation of Life Technologies' Ion Torrent AmpliSeq Cancer Panel via its CLIA-certified laboratory (CSN 1/16/13).
"Expectations are high, and our job is to live up to the promise [of sequencing] to help identify novel targets for patients who may not have any choices with respect to treatment. And also to make discoveries that may be useful for a larger population," Rubin said.
While running the new Weill Cornell Institute, Rubin is also leading an upcoming effort with the University of Michigan and five other centers to use mutation information from patients' prostate cancer exomes to predict their response to current and developing therapies.
The project was awarded a $10 million, three-year grant last spring by Stand Up To Cancer and the Prostate Cancer Foundation (CSN 7/19/2012).