Sunday, January 12, 2014

Aiming to Push Genomics Forward in New Study

from nytimes

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Dr. George D. Yancopoulos of Regeneron said the cost of DNA sequencing had dropped sharply. Gregg Vigliotti for The New York Times
Here comes genomics, Take 2.
Pharmaceutical companies invested heavily in genetic studies in the frenzy after the sequencing of the human genome a decade ago, only to find it did not lead to the expected bonanza of new drugs.
Now, however, Regeneron Pharmaceuticals, a fast-growing biotechnology company, is undertaking an ambitious new genomics effort, in partnership with the Geisinger Health System, which treats three million people in Pennsylvania.
Regeneron will sequence DNA from about 100,000 volunteers among Geisinger’s patients, seeking genetic variants linked to different diseases that may provide clues to developing new drugs. Geisinger, in turn, hopes to use the genetic information to improve patient care.
“Scientifically and medically, it’s pretty exciting,” said Dr. Leslie G. Biesecker, chief of the genetic disease research branch at the government’s National Human Genome Research Institute, who is familiar with the project. “As far as I’m aware, it’s the largest clinical sequencing undertaking in this country so far by a long shot.” He added that the move of sequencing into general health care “is going to change medicine.”
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A technician in Regeneron’s new research center in Tarrytown, N.Y. Gregg Vigliotti for The New York Times
Dr. George D. Yancopoulos, the chief scientific officer of Regeneron, said the plummeting cost of DNA sequencing and his own company’s scientific capabilities point toward a more successful effort this time.
“We think we are the right one that can address a lot of the limitations that have kept this from turning into reality before,” he said. Regeneron has opened a genetics research center in Tarrytown, N.Y., where the company is based.
It now costs several thousand dollars to sequence a complete genome, meaning to determine the order of the three billion chemical units of DNA — usually represented by the letters A, C, G and T — in a person’s chromosomes. Even that is still too expensive for a project of this scope. So at first Regeneron will sequence just the exome, the 1 to 2 percent of the DNA that contains the recipes for proteins. A complete exome can be sequenced for less than $1,000.
Similar projects are also beginning, though mostly in the public sector. Britain and Saudi Arabia have each announced plans to sequence 100,000 genomes. The United States Department of Veterans Affairs plans to collect DNA from one million veterans. Various medical centers and health systems have smaller projects.
The biotechnology giant Amgen paid $415 million about a year ago to acquire deCODE Genetics, which had determined, partly through calculations, the genome sequences of 300,000 people in Iceland.
Dr. Yancopoulos might be excused his brashness in predicting success. After two decades of setbacks in developing drugs, Regeneron has broken into the top ranks of the biotechnology industry with its blockbuster product, Eylea, which was approved in 2011 as a treatment for the eye disease called age-related macular degeneration.
Dr. Yancopoulos, who has been at Regeneron since 1989, shortly after the company was founded, earned more than $80 million in compensation in 2012, mostly from stock. The company’s founder and chief executive, Dr. Leonard S. Schleifer, was ranked last year by Genetic Engineering and Biotechnology News as the life science industry’s third-wealthiest executive, based on the $1.13 billion worth of Regeneron stock he held.
Regeneron and its partner, Sanofi, are in a race against Amgen to be the first to market with a powerful type of cholesterol drug that works by blocking the activity of a protein called PCSK9.
The drugs are based on human genetic discoveries of exactly the type Regeneron hopes to make with its new project. This discovery, however, came from academic scientists who found that people with mutations in the PCSK9 gene had extremely low cholesterol.
David B. Goldstein, a professor of genetics at Duke University, applauded Regeneron’s effort, but said it might be hard for the company to beat academic centers in finding important mutations. “I don’t think there’s a tremendous proprietary value,” Dr. Goldstein said.
Dr. Yancopoulos agreed in part, saying that many of Regeneron’s findings would be made public anyway. But he said the company would have an advantage in developing drugs because it would be the most familiar with the data and because it had leading technology for putting human genes into mice for use in experiments.
The previous generation of gene-hunting studies sampled the DNA of people at particular spots in the genome. Those studies found many common genetic variations that raise or lower the risk of various diseases, but only by a small amount.
The new projects, by sequencing the entire exomes or genomes of huge populations, are looking for rarer variations that might have a bigger influence on disease risk.
“You want the low-frequency, high-impact variants because they are the ones that are going to have more impact on the biology,” said Dr. Jeffrey Gulcher, chief scientist at NextCODE Health, a deCODE spinoff that sells software and services for genomic studies.
Studies trying to link genes to diseases require information on the health of the people whose DNA is being studied. That is where Geisinger comes in. It has extensive electronic medical records on its patients and has already collected 45,000 DNA samples.
To protect patient privacy, the medical information and DNA samples given to Regeneron will be anonymous. But Geisinger will know who the patients are and can use that information in their care.
For instance, if the sequencing finds that a patient has a mutation indicating a high risk of getting breast cancer, the person might be informed and steps might be taken to prevent the disease, said David H. Ledbetter, a geneticist and chief scientific officer at Geisinger. Certain mutations could also provide information helpful in choosing the best drug treatment for the patient.
Regeneron and Geisinger did not disclose financial details of the arrangement. Sequencing 100,000 exomes will probably cost about $100 million over five years, an amount Regeneron can easily handle.
Regeneron will also pay Geisinger, but the health system said it was not selling its patients’ DNA and medical information for a profit. “They are covering our cost,” said Dr. Glenn D. Steele Jr., the chief executive of Geisinger.
He said Geisinger knew it would need genetic information to provide better care, but decided to “farm out” the “factory work” of sequencing and that the health system would share in the proceeds of any drugs developed from the information. Regeneron said it might also collaborate with other academic centers and health systems.

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