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Cancer Center To Sequence Genomes

ALBUQUERQUE, N.M. — The University of New Mexico Cancer Center this fall will be among the first 20 sites worldwide to acquire a technology that can sequence an entire human genome in half a day for about $1,000, giving doctors a powerful new tool for diagnosing and treating cancer, UNM researchers said.

The Cancer Center expects to get the new equipment by October and begin using it to sequence the DNA of New Mexico cancer patients by early next year.

“We’re trying to move this technology to the clinic and actually have it play a role in the treatment of a patient,” said Jeremy Edwards, a UNM professor of molecular genetics and biology who helped develop the technique.

The Cancer Center’s initial plan is to sequence the DNA of about 100 patients in the first year, with a focus on leukemia, colorectal and breast cancer patients enrolled in a clinical study.


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“The use of whole genome sequencing is just being introduced for cancer patients,” said Cheryl Willman, director and CEO of the UNM Cancer Center. Fewer than a dozen cancer centers now use genome sequencing for clinical purposes, but many others are considering the technology, she said.

“We want to use it because studies are beginning to show that cancers have so many genome mutations that the best way to develop a therapy is to understand the profile of mutations in the cancer cells,” Willman said.

The human genome consists of about three billion DNA bases, or rungs in a ladder-like structure. Genome sequencing maps the complete DNA structure and can identify genetic changes, or mutations, that can cause disease.

But whole genome sequencing raises a thicket of legal, social and ethical questions because the technique can reveal diseases and conditions previously unsuspected by patients and their families, Willman said.

The new technique will require UNM to form oversight and advisory panels to steer doctors and patients through potentially thorny issues such as how patients should be informed about genetic conditions revealed by the tests, she said.

Whole genome sequencing now costs UNM about $10,000 per patient and requires at least two weeks of work by an out-of-state company, Edwards said.

The human genome was first mapped by the Human Genome Project – an international collaboration that took 13 years, beginning work in 1990 and finishing in 2003.

The new technology, called an Ion Proton Genome Sequencer, uses computer technology that can analyze 600 million DNA samples on a single silicon chip, Edwards said. UNM will pay about $150,000 for the equipment.

“It’s basically a computer chip that does the DNA sequencing,” he said. Edwards and others at UNM have worked since 2010 with prototypes of the new technique.

The technology “is leveraging the semiconductor industry, which has learned how to make things very fast and very cheap.”

The new technique will allow researchers to quickly sequence DNA from both healthy tissue and a cancerous tumor and compare them to identify harmful mutations.

At first, the mass of genetic data likely will present more questions than answers, Edwards said. But he predicted that physicians will learn how to use the new tool to make drugs that target harmful mutations.

“More and more data will be collected, and we will eventually be able to tailor therapies to each individual,” he said. “That will probably happen over the next three to four years.”