Friday, May 25, 2012

Computing cluster speeds targeted treatments for childhood cancer

AUSTIN – Cloud-based research technology launched by Dell last year for the Translational Genomics Research Institute (TGen) is gearing up for what's billed as the world’s first precision medicine clinical trial for pediatric cancer.

James Coffin, vice president and general manager, Dell Healthcare and Life Sciences, says the eight-teraflop supercomputer, billed as the "kids cloud," will drastically reduce the time required to identify personalized treatments for children participating in the trial program – kids who have no time to spare. In turn, that acceleration can help open the trials up to participation from more children.

The Human Genome Project "took $3 billion and 10 years" to sequence the first genome, he points out. "A year ago, it took about nine months and cost about $400,000 or $500,000 to do a full genome."

And recently, says Coffin, "we just ran a test for a full genome for a patient, and got all the the results and made a clinical decision for the patient to the tumor board in less than five days."

Dell has "done a lot of work to retune the codes and make them run really fast on this platform," he says. "Just three months ago, the analysis of 25 million bases – there's usually about 500 or 600 million bases you have to do to kind of do this whole genome sequence – and 25 million bases took about 48 hours."

Now, that time is down to six hours.

"There's an inflection point in genomic science right now, where we have these new, next generation sequencers that are coming out over the last six months from companies like Illumina and Life Technologies, and then we have very very fact computing, and new processors coming out from Intel," says Coffin.

"I've been talking about personalized medicine for 13, 14 years, since before the human genome project happened, saying that this is the future of medicine," he adds. "It's here now."

Oncologists from the Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC) and biomedical researchers from TGen will use Dell's computing and collaboration cloud to seek out and ID treatments for pediatric cancer patients based on the specific genetic vulnerabilities of each specific tumor.
First announced in November 2011, Dell’s team has completed the high performance computing cluster that will serve as the cloud’s computational foundation and basis for a private cloud, officials say. When equipped with Dell’s PowerEdge M420 server technology, TGen can analyze comprehensively a patient’s tumor RNA profile seven times faster than was previously possible. Time, of course, is a precious commodity for kids with cancer.

"With this particular population of children, with pediatric neuroblastoma, you've essentially got one shot," says Coffin.

With the dedicated computing cluster in place, Dell will begin to connect the biomedical researchers sequencing and analyzing patient tumors at TGen in Arizona with oncologists providing treatment to patients participating in the trial at 11 medical centers, officials note, adding that the new cloud will eliminate the need to express mail hard drives containing tumor and diagnostic images and genomic sequencing data between locations.

[See also: Slideshow: Advances in personalized medicine.]
With just one new treatment for pediatric cancer approved by the FDA since the 1980s – compared with 50 treatments approved for adult cancer in the same period – pediatric oncologists have often been forced to rely on adult-sized treatments, leading to some toxic side effects that are often as harmful to children as the cancer itself. More targeted treatments can aim right for the specific vulnerabilities of each child’s tumor, leaving healthy cells untouched.

"We're really making progress and figuring out what the cocktail is for them very quickly," says Coffin. "We're able to go full genome sequence on them and really get all the information we think we need. It's a very different game."

In the coming years, the hope it that this approach can not only be "a model for all cancer" but "a way to treat all disease," says Coffin. "Understanding the biological and genomic pathways of these things is the way you need to treat everything going forward."

He adds that "this is one of the reasons I'm so passionate about healthcare IT. This is the kind of thing health IT can do to change the world. I don't think health IT gets enough credit for what it does. This is a perfect example: you can't do this without health IT."

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