Grappling With the Genome: Cancer Centers Approach Puzzle in Different Ways

Andrew D. Smith
Published: Monday, Jun 11, 2012
Tumor tissue samples await analysis for cancer-related genes

Photo courtesy of the Dana-Farber Cancer Institute.

Tumor tissue samples await analysis for cancer-related genes at the Center for Advanced Molecular Diagnostics at Brigham and Women’s Hospital.

As the cost of sequencing and analyzing genetic data continues to fall, the nation’s leading cancer centers keep unveiling ambitious new clinical programs and research projects that will change the way every cancer specialist practices.
Dana-Farber Cancer Institute, along with Brigham and Women’s Hospital, has launched one of the biggest research programs to date, in which the Boston, Massachusetts, centers seek to make the tumors of every patient with cancer a subject of genetic research.

Other cancer centers, while not broadening the research pool so widely, have deepened it by analyzing multiple tumor samples from each patient or conducting full-genome sequencing of both tumor samples and healthy tissues in tested patients.

These research projects supplement rapidly evolving protocols for clinical care. The tumors of most patients at most major facilities now receive some form of genomic testing to guide treatment. And that testing keeps getting more detailed.

For oncologists, hematologists, and other specialists who treat patients with cancer outside academe, these trends portend more than just an avalanche of studies that will have to be read. They portend a whole new age, albeit one that’s still a bit hazy.

Dr. Gordon B. Mills

Gordon B. Mills, MD, PhD

“Genetic analysis has already changed cancer care at every practice, and we’ve only seen the tiniest tip of the iceberg,” said Gordon B. Mills, MD, PhD, who chairs the Department of Systems Biology and holds the Olga Keith Weiss Distinguished University Chair for Cancer Research at The University of Texas MD Anderson Cancer Center in Houston.

“But I think we have a little work to do before we know how we can best use these new tools,” he said. “Different cancer centers are trying different things, which will help us figure out what works and what doesn’t, and what all cancer specialists should eventually be doing.”

Sequencing Costs Plummeting

Ever since the Human Genome Project resulted in the full sequencing of the first human genome in 2003, technological advances have increasingly enabled researchers to explore the genetic underpinnings of cancer at a decreasing cost.

“The ability to sequence an individual’s entire genome as well as the patient’s tumor genome is now a feasible enterprise at a cost and speed that was unthinkable even five years ago,” noted Boris Pasche, MD, PhD, of the University of Alabama in Birmingham, and Devin Absher, PhD, of the HudsonAlpha Institute for Biotechnology in Alabama, in an editorial in the Journal of the American Medical Association last year.1

Indeed, it took 10 years and more than $2 billion to sequence the first human genome. Today, whole-genome sequencing costs from approximately $10,000 to $35,000 per human genome, and the National Institutes of Health (NIH) $1000 genome target is within the realm of possibility.2

Researcher using a pipette to prepare DNA for sequencing

Photo courtesy of Maggie Bartlett/National Human Genome Research Institute

A researcher at the National Human Genome Research Institute uses a pipette to prepare DNA for sequencing.

Meanwhile, the nation’s network of cancer centers has been gearing up to make the most of the new technology, both individually and with federal leadership. After the genomic changes that occur in gliobastoma and ovarian cancers were successfully mapped, the NIH launched The Cancer Genome Atlas project in 2009. More than two dozen institutions throughout the country are working on characterizing, sequencing, and analyzing the genomes of more than 20 cancers.3


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