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Duke Details Plans for Restructured Genome, Policy Centers

NEW YORK (GenomeWeb) – By the time the fall semester rolls around at Duke University this year, the school's decade-old flagship genomics program, the Institute for Genome Sciences and Policy, will be gone

This summer its administrators are breaking the Institute down and restructuring it into three separate units. Each of the new entities will engage with scientists from all over the campus in interdisciplinary projects that reflect the expansion of genomics into broader realms.

When the plan to break up the IGSP was unveiled in March, then IGSP Director Huntington Willard said the goal was to create distinct centers that would be able to address some of the changing areas of genome science, technology, and policy

The three new units include a translation-focused Center for Applied Genomics and Precision Medicine, a core facility tentatively named the Center for Genomic and Computational Biology, and Duke Science and Society, a free-standing policy and ethics institute that will address a broad swathe of scientific issues.

The leaders of the new units, who were already directing their respective activities within the IGSP, recently told GenomeWeb Daily News that they are still working out a few details for their divisions, but that they will continue to pursue missions that have long been underway.

Targeting translation

The Center for Applied Genomics and Precision Medicine will aim to take genomic and biomarker-driven translational discoveries from the germinal phase all the way to the clinic.

The center's Director, Professor Geoff Ginsburg, formerly ran both of the IGSP's genomic medicine units. These included one center that pursued early-stage translational science aimed at moving research into the clinic, and another that advanced science toward actual clinical practice through implementation studies and outcomes research, he told GWDN. These programs, which Ginsburg estimates reeled in around $70 million in grants over the last decade, will now join to conduct a full range of translational genomics studies.

"This is going to be very much a continuum that is focused on diagnostics and decision-making around patient care," he said.

Ginsburg's group, which currently has around 10 faculty members and 25 full-time staff members, is disease-agnostic but has had an emphasis on cardiovascular disease, he said, and these scientists have already been engaged in a wide range of translational projects that cut across the different disciplines of genomic medicine.

Teams at the two IGSP centers worked on the gene expression profile discovery effort that eventually led to the CardioDx Corus CAD test, and their pharmacogenetics program was involved in identifying genetic variants that are involved in statin efficacy and safety, Ginsburg said.

His groups also have conducted research for the US Department of Defense on the use of genomic technologies to predict and diagnose the etiology of infectious diseases.

"We now have an entire portfolio of gene expression profiles that can distinguish viral infections from bacterial infections from fungal infections based solely on host response," he explained. That group is now working on clinical studies to demonstrate the utility and validity of these profiles.

One ongoing and "very large" program focused on systems pharmacogenomics and antiplatelet agents, is using genomics, RNA sequencing, proteomics, and metabolomics approaches to understand the myriad pathways that aspirin and other antiplatelet drugs hit, Ginsburg said.

These projects also include a family history software platform called MeTree that captures information from patients in their homes and delivers clinical decision reports about their risks for 20 different conditions. The goal is that doctors can use it to decide if their patients should see a genetic counselor, have an additional evaluation, or take a genetic test.

"We think this is going to be a significant game changer in how providers actually assess risk in otherwise healthy patients," Ginsburg said.

"What it boils down to," he told GWDN, is that the center seeks to make discoveries that "have an impact … on a clinical decision that ultimately may change the way that healthcare is delivered."

Some of the efforts will be clinical research studies to show how genomic-based biomarkers correlate with various phenotypes and clinical outcomes, and then trying to evaluate how they impact patient care.

"The big question in genomic and personalized medicine today is: what is the value proposition? Does it actually create value and should it be adopted and reimbursed and possibly have regulatory approval? [This center] also will focus on those types of things," said Ginsburg.

All things genomics

The facilities and staff from IGSP's core genomics lab and computational unit will now be consolidated to form the tentatively-named Center for Genomic and Computational Biology, Professor Greg Wray, who will direct this center, told GWDN. This center will provide core resources, education and training, and computational biology services to scientists from all corners of the campus, including those involved in medical, engineering, environmental, and natural sciences research.

"We are the resource on campus for all things genomics, both on the analysis side and the data-generating side," said Wray, who previously directed the IGSP's sequencing core for about 10 years, or "since before there was next-gen sequencing."

In terms of dollars, staff, and client base, the sequencing lab with a staff of seven will be the largest piece of this center and will provide a range of omics and computational services to investigators on and off campus via "all the current major" sequencing platforms. The center's suite of services include whole genome sequencing, library prep, genotyping, resequencing, proteomics, metabolomics profiling, expression analysis, quality control, association mapping, and epigenetics.

"We're more of a bespoke [lab]… We tend to work closely with investigators to tailor their projects," Wray said.

Through its information technology component, the center also will help researchers build databases and provide modeling, simulation, mapping, and de novo assembly services.

Wray says the center's services reflect the expansion of genomics into a broader range of disciplines, and that it will serve basic scientists and clinicians engaged in all types of research, some of whom have varying skill sets, budgets, and comfort levels with the technologies.

Wray said the center also will serve as a project incubator. "We're an incubator for ideas. We go out and partner with other units," he said. "Someone in our department may write a grant with someone in surgery, or in electrical engineering, or with somebody in biology. We're bringing the experience and the capability to get those projects off the ground immediately."

"By having the core facilities and a lot of very entrepreneurial young faculty come in and train as genome scientists – some of those are from engineering, the medical school, arts and sciences, statistics, and computer science, we have an environment where we throw them into one space and just have them interface with each other and try to find the synergies," Wray told GWDN.

A national conversation

The final segment that has launched from the former IGSP is a science policy institute, Duke Science and Society, headed by Professor Nita Farahany, who also is a member of the Presidential Commission for the Study of Bioethical Issues.

Farahany formed Duke Science and Society within IGSP last summer with the intention of splitting off this summer into a free-standing university institute that would address an array of science issues ranging far beyond genomics.

The institute places an emphasis on its education efforts – it is launching a master's program in bioethics and science policy this fall that includes a genomics track – and on communicating science issues. It also houses research projects that delve into the inter-relationships between science and society at the legal, political, and personal levels.

One vision for this institute is that it will enable Duke faculty members to join the "national conversation" about science policy and bioethics, and to help shape science policy, Farahany told GWDN.

Although Duke Science and Society does not house the wet labs or hardware, it does have genomics policy experts, some working on projects funded by the National Human Genome Research Institute. Some key members of the staff, which has about 15 to 20 faculty members and 130 affiliated faculty, have long been involved in shaping the national conversation about genomics. Misha Angrist, an assistant professor of the practice who leads Duke Science and Society's Public Impact and Engagement track, has for years commented on and researched issues surrounding human participation in genomics research and medicine. Robert Cook-Deegan, a research professor of public policy, internal medicine, and biology, has written about a panoply of genomics policy issues over the past two decades, and is an expert on genetic intellectual property issues. Meanwhile, instructor Sara Katsanis' work has focused on policy options for genetic testing applications, such as direct-to-consumer genetic testing, pharmacogenetics, drug labeling, and related issues. Farahany said these and other genomics policy experts will join in and drive the national discourse about genomics.

Beginning this fall, this institute also will house a communications program to help researchers engage with the public, and will train them to talk science with lawmakers and send them to Capitol Hill to do just that.

"So, when something such as the Food and Drug Administration's decision around direct-to-consumer genetic testing comes up, we would take faculty who have been trained in the science education program to the Hill to brief different people who are involved in that decision-making on the issues, and on the science," Farahany explained.

She said Duke Science and Society will not be "genomic exceptionalists," but rather it will recognize "that a lot of issues faced by researchers in genomics are faced similarly by researchers in other areas, like neuroscience and engineering."