Breast cancer genome study launching

Breast cancer genome study launching
Carlsbad firm hopes to find best treatment for 14 patients
By Thomas Kupper, UNION-TRIBUNE STAFF WRITER

Friday, March 5, 2010 at 6 a.m.


Life Technologies research associate Joshua Shirley and senior scientist Gothami Padmabandu used one of the company's machines that can detect the swine flu virus. (Charlie Neuman / Union-Tribune)


A Carlsbad biotechnology company is helping launch an unusual cancer study that may eventually lead to doctors tailoring treatments to patients’ genes.

Life Technologies says the study — involving sequencing the genomes of 14 patients with a tough-to-treat form of breast cancer — is a step toward a future of “genomic medicine,” a decade after the sequencing of the first human genome.

It’s evidence of how quickly work in this area is progressing, with the $2.6 billion that went into the Human Genome Project reduced to $6,000 per genome on Life Technologies’ latest sequencing instrument.

“This is a pretty amazing example of how far these tools of genomics are moving into direct patient applications,” said Jeffrey Trent, president of the Phoenix-based Translational Genomics Research Institute, which is working with Life Technologies on the project.

The company will announce the study today to coincide with the opening of a two-day conference on genomic medicine in La Jolla, at which experts will discuss the latest breakthroughs and the outlook for more advances in the field.

Already, biotechnology research has created numerous drugs that target genetic problems that lead to cancer and other conditions. In the case of breast cancer, at least a dozen such drugs are on the market, said Dr. Daniel D. Von Hoff, physician-in-chief at the translational genomics institute.

A big problem, however, is that it’s difficult to predict which drugs will work for a particular patient. That’s where sequencing is supposed to help.

“For those mutations for which we do have drugs, we can help the physician make more informed decisions than they’re making today,” said Linh Hoang, director of personalized medicine at Life Technologies.

The study could also help scientists identify promising areas to explore for future drugs.

It’s impossible to know ahead of time whether the 14 patients have genetic patterns that current drugs address, but researchers will also look for similarities in the DNA of the 14.

“It may lead to more targets that pharmaceutical companies will want to design drugs around,” Hoang said.

The study will involve patients with what’s known as triple-negative breast cancer whose tumors have progressed despite multiple therapies. That type of cancer makes up about a fifth of breast cancer cases and doesn’t respond to common drugs, such as Herceptin.

Patients will be enrolled by U.S. Oncology, a Houston-area company that specializes in cancer-treatment services, and Von Hoff said the plan is to take the first 14 people who meet the study criteria.

A spokeswoman for U.S. Oncology said the company plans to enroll patients from about a half-dozen of its sites with the highest incidences of triple-negative cases. Sites in Colorado, Oregon, Texas and Virginia have already been identified.

Tissue samples will be obtained through noninvasive surgery, Von Hoff said. Then the patients will go home to await sequencing results that should be produced within a few weeks.

The idea is to then direct them to appropriate treatment, but Von Hoff declined to predict in how many cases that will be possible.

“We don’t know,” Von Hoff said. “We do know there are more and more drugs out there for patients who have mutations.”

There have been other studies that sequenced disease tumors, most notably an ongoing government effort known as the Cancer Genome Atlas that aims to produce comprehensive genetic maps of at least 20 types of cancer.

What separates the new study is its attempt use the data to drive treatment strategies, not merely to collect information.

“It’s a different question,” the genomics institute’s Trent said. “This is a study about how we’re going to start to use this in a precision medicine approach.”

A big effort will go into “bioinformatic” analysis, which Von Hoff said will involve a trillion pieces of data per patient. Hoang said one project in lung cancer found 30,000 mutations.

In coming years, scientists expect the cost of sequencing to decline and the sophistication of the tools to improve to the point that sequencing becomes more viable as a diagnostic device.

Hoang said Life Technologies expects the cost of the reagent chemicals that it sells, which enable genome sequencing, to drop from $6,000 to $3,000 by the end of the year.

“This is really laying the foundation for a future that may take five or 10 years to materialize,” Hoang said. “But it is truly groundbreaking.”

OVERVIEW
Background: Drug companies have developed an array of drugs to attack cancer and other conditions influenced by genetics, but it’s difficult to tell which patients will respond to which drugs.

What’s happening: A new study will sequence the genomes of cancer tissue from 14 breast cancer patients whose tumors have progressed despite multiple treatments.

The future: Proponents of “genomic medicine” think it will become increasingly possible to use sequencing to steer individual patients to the drugs most likely to work.
Thomas Kupper: (619) 293-1037; thom.kupper@uniontrib.com
http://www.signonsandiego.com/news/2010/mar/05/breast-cancer-genome-study-launching/