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Posts Tagged ‘Eric Green’


ENCODE (Encyclopedia of DNA Elements) program: ‘Tragic’ Sequestration Impact on NHGRI Programs

Reporter: Aviva Lev-Ari, PhD, RN

NHGRI’s Green Sees ‘Tragic’ Sequestration Impact on NHGRI Programs

September 13, 2013

NEW YORK (GenomeWeb News) – The funding squeeze from the sequestration of the US federal budget, now more than half-a-year old, has already had a sizable impact at the National Human Genome Research Institute, leading to cuts to ongoing programs, scaling back of new ones, and the deferring of efforts that have not yet launched.

The five percent cut in funding this year at NHGRI has led not only to trimmed-down renewal grants and fewer, smaller awards broadly, but also has chopped the budget for some of the institute’s important programs, according to NHGRI Director Eric Green.

The programs that have either had their funding reduced, and in one case delayed, include the ENCODE (Encyclopedia of DNA Elements) program, projects focused on using genome sequencing in newborns and in clinical medicine, and other initiatives, Green said in his Director’s Report to the National Advisory Council on Human Genomics Research this week.

In addition, many renewal grants have been trimmed, and there are “numerous examples of detrimental cuts” to the institute’s intramural research program, said Green. These cuts to large and small NHGRI programs come at a pivotal time for genomics, he noted, as the products of such research are beginning to translate into clinical possibilities.

“It is tragic. [That] is the word I would use,” Green told GenomeWeb Daily News this week.

“[The field of genomics] is just so exciting. There are so many opportunities,” he said. “This is precisely the time that we should be pushing the accelerator hard, and we just cannot do it because we don’t have enough fuel in our fuel tank.

“It’s frustrating. I think the opportunities now are just spectacular,” said Green. “It’s tragic because it is just so obvious that we could do some remarkable things in genomics and we are not being able to do it.”

ENCODE, a decade-old flagship project at NIH that aims to identify all of the functional elements in the human genome, had its budget reduced by 16 percent.

The Genomic Sequencing and Newborn Screening Disorders program was cut by half, which left the program to fund fewer research projects than planned and its research consortium to go forward without the benefit of a data coordinating center. This new initiative, an effort to support pioneering studies on how sequencing might be used in the care of newborns and in neonatal care that was created jointly with the Eunice Kennedy Shriver National Institute of Child Health and Human Development, had its budget cut from $10 million to $5 million.

The Genomic Medicine Pilot Demonstration Projects program had its budget cut by 20 percent, and NHGRI’s Bioinformatics Resources and Analysis Research Portfolio had $5 million sliced out of its budget. The new Genomics of Gene Regulation (GGR)request for applications was bumped out of this funding year entirely, and has been delayed until 2014, according to Green.

Because the sequestration plan was concocted and agreed to well in advance of its arrival earlier this year, Green told GWDN that the institute did have some time to try to react to the sequestration and mitigate the pain from the cuts, spreading them around fairly and evenly while maintaining priorities. He said leadership at the institute tried to prepare for the possibility of sequestration by being conservative in its planning.

Programs that were already ongoing, like ENCODE, were likely to take priority over those that were not yet launched, like GGR, in part because the infrastructure is already in place for ongoing projects and because it is easier to plan for how they operate and generate outputs, like data.

“With ENCODE you know for every million dollars you invest you get so much back,” said Green. “With a program like newborn sequencing … we don’t totally know what it’s going to look like or play out like. We won’t know what we are missing because we won’t be able to launch it to the scale that we wanted to launch it originally.”

Green said some of the projects being cut or delayed were created under NHGRI’sstrategic plan, a program it laid out in 2011 that involves restructuring of the institute’s divisions and some shifting in its research portfolio to include more efforts in applying genomics to medicine and healthcare.

“Some of these RFAs that we delayed really represent key elements that we started to anticipate two years ago,” said Green. “We knew we wanted to do more in sequencing, we knew we wanted to do some pilot projects in genomic medicine. We knew we wanted to continue to accelerate efforts in understanding how the genome works … ENCODE, GGR, and so forth. It just had to be slowed down,” he said.

Anastasia Wise, program director for the Genomic Sequencing and Newborn Screening Disorders program, told GWDN that the program was supposed to be much larger than the $5 million in awards unveiled last week, which funded a consortium of four research projects.

Wise said NHGRI and NICHD were each initially planning to provide double the amount of funding they were actually awarded, which is now expected to be a total of $25 million over five years, although that total could be subject to the availability of funding.

“There were definitely more scientifically meritorious applications than we were able to fund,” she said. “Even the four awards that we made ended up being cut an additional five percent because of the sequestration.”

She said the program “wanted to be able to make more awards, and we wanted to be able to fund a coordinating center to be able to bring the network together and help provide some harmonization of data and coordination of logistics between the different members of the consortium,” but it was unable to fund that part of the effort.

Although the fractured fiscal culture in Washington engenders caution at NHGRI as the agency looks forward, Green sees many scientific opportunities right now, as genomics begins to hit the clinic.

“Some people are saying we are not even going fast enough,” he said. “Lots of people have been discussing what the world is going to look like when somebody gets their genome sequenced in the newborn period, and [they] think about what the implications of that are for the patient for the rest of their lives. We want to start studying this,” he said.

“And we are starting to … but we’re not starting as aggressively as we wanted to,” Green said. “I mean, we took a big hit this year.”

Matt Jones is a staff reporter for GenomeWeb Daily News. He covers public policy, legislation, and funding issues that affect researchers in the genomics field, as well as the operations of research institutes. E-mail Matt Jones or follow GWDN’s headlines at @DailyNewsGW.

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Reporter: Aviva Lev-Ari, PhD, RN

The reader is encourage to review the following ANALYSIS of this subject matter:

Genomics & Genetics of Cardiovascular DiseaseDiagnoses: A Literature Survey of AHA’s Circulation Cardiovascular Genetics, 3/2010 – 3/2013

and

10 Years On, Still Much To Be Learned From Human Genome Map

Advances made in genetics of disease, but creating new drugs more complex than first thought

By Amanda Gardner
HealthDay Reporter

FRIDAY, April 12 (HealthDay News) — As scientists mark the 10th anniversary Sunday of the completion of the Human Genome Project, they will note how that watershed effort has led to the discovery of the genetic underpinnings of almost 5,000 diseases.

And it has made it possible to develop personalized treatments that have prolonged the lives of many.

But the scientists will also acknowledge that, while the project has unlocked many mysteries that once shrouded diseases, there’s still much to be learned before new drugs can be developed to target illness-causing mutations in human DNA.

“What we’ve learned over the past 10 years is that we’re still far from really understanding the complexity of the human genome,” said Eric Schadt, chairman of genetics and genomic sciences at Mount Sinai Icahn School of Medicine in New York City. “Human disease is way more complicated than the old view that single hits to single genes cause diseases.

“In most forms of diseases, it’s whole constellations of genes operating in networks,” Schadt explained. “That becomes a much harder problem. How do you target networks with a single drug?

“We keep learning how much we really don’t know and how much further we need to go,” he added. “That’s the big story.”

A decade ago, the Human Genome Project was hailed as a major milestone because researchers identified all of the nearly 25,000 genes in human DNA and sequenced the 3 billion chemical base pairs comprising that DNA.

The feat took 13 years and cost close to $3 billion, but the genetic information gleaned from the project gave scientists the tools needed to pinpoint how changes in specific genes could kick-start some diseases.

One of the most tangible benefits of the project has been the development of ever more sophisticated sequencing technology and a dramatic lowering of the cost of using that technology.

Today, the cost of sequencing one human genome is closer to $5,000 and can be done in a day or two, said Dr. Eric Green, director of the National Human Genome Research Institute in Bethesda, Md.

What that means is that the pace of research, and its attendant discoveries, has been accelerated.

When the project first began, scientists knew the genetic basis of about 53 diseases. Today, that number is close to 5,000, Green noted. That means doctors can now test patients to see if they carry gene mutations that raise their risk for certain diseases, and counsel them accordingly on ways they might prevent or delay illness. There are currently almost 2,000 genetic tests for specific diseases or conditions, according to the U.S. National Institutes of Health.

There have also been breakthroughs with some rare diseases.

In 2011, 6-year-old Nicholas Volker became the first child to be saved by the new technology. He had undergone a hundred surgeries, including the removal of his colon, as doctors tried to identify his mysterious bowel disease. Genomic sequencing uncovered a genetic mutation that could be treated with a bone marrow transplant consisting of cells from umbilical cord blood.

“Knowing more of the basic genetics that makes up an individual has allowed us to diagnose far more genetic diseases,” said Dr. Barbara Pober, a medical geneticist at the Frank H. Netter, M.D. School of Medicine at Quinnipiac University in North Haven, Conn.

Once a diagnosis has been made, doctors can now use gene sequencing to determine treatment for some diseases. For instance, breast cancer patients can be tested to see how they will respond to the drug Herceptin. HIV patients can be tested to determine their response to the drug abacavir. And those on the widely used blood thinner warfarin can be tested to determine the most effective dose, according to the NIH.

The field of pharmacogenetics, still in its infancy, enables doctors to use a patient’s genetic information to figure out which cancer drugs the patient will best respond to before treatment even starts.

The U.S. Food and Drug Administration now includes genetic information on labeling for more than 100 drugs, up from just four 10 years ago, Green said.

The goal of developing new drugs to target diseases with genetic roots, however, will take much longer to realize.

Although the NIH states that there are roughly 350 biotechnological products currently being tested in clinical trials, new drugs take a decade or more to develop. Not only that, the knowledge gained from the Human Genome Project has actually made the field of genetic medicine even more complex. Scientists are finding that many diseases are triggered by interaction involving multiple gene variants, making it difficult to design a treatment that targets all the culprits in a particular illness.

And the complexities don’t end there.

Not long ago, scientists discovered that so-called “junk” DNA, which makes up 98 percent of the genome, is not junk at all but serves critical regulatory functions.

What’s more, about 10 percent of the human genome still hasn’t been sequenced and can’t be sequenced by existing technology, Green added. “There are parts of the genome we didn’t know existed back when the genome was completed,” he said.

More information

For more on developments over the past 10 years, visit the Human Genome Projectwebsite.

SOURCES: Eric Green, M.D., Ph.D., director, National Human Genome Research Institute, Bethesda, Md.; Barbara Pober, M.D., professor, medical sciences, Frank H. Netter, M.D., School of Medicine, Quinnipiac University, North Haven, Conn.; Eric Schadt, Ph.D., professor and chairman, department of genetics and genomic sciences, Mount Sinai Icahn School of Medicine, New York City

Last Updated: April 12, 2013

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