More-accurate cancer tests based on same math as digital age

In In The News by Barbara Jacoby

By: John Shinal


A more-accurate, less-invasive cancer test now on the market is based not only on genomics but on the same mathematical theories underlying data communication.

The test from Guardant Health can detect trace amounts of cancer DNA in the bloodstream.

The idea behind it has a common origin with signal processing and other technologies that became “the basis for our digital society,” says Professor Abbas El Gamal, chair of the electrical engineering department at Stanford University.

Trying to filter and compress digital data over copper wires or wireless systems has something in common with sifting through massive amounts of genomic data looking for cancer, he says.

“It’s about extracting information from noisy signals,” says El Gamal, whom I’d called to ask about his former student, Helmy Eltoukhy, now CEO of Redwood City, Calif.-based Guardant.

The company’s Guardant 360 test was approved for commercial use last year.

A blood test rather than a biopsy, it’s easier on patients than existing procedures that extract and test samples of human tissue.

It’s also 97% accurate and is being used by leading oncology centers from coast-to-coast, including at Thomas Jefferson University in Philadelphia, the University of Texas MD Anderson Cancer Center in Houston and the University of California, San Francisco.

At a molecular medicine conference here this week, several speakers discussed early diagnostic successes using new, genomic-based cancer tests.

“We’ve been able to detect cell-free, tumor-specific DNA (or ctDNA) in a large number of advanced and localized malignancies,” wrote Chetan Bettegowda, assistant professor of neurosurgery and oncology at Johns Hopkins University, in a summary of his keynote presentation to the gathering, MolecularMed Tricon 2015.

Stanford’s El Gamal says the detection technology of such tests can be traced all the way back to the theoretical work of Claude Shannon.

In 1948, while he was an engineer and mathematician at Bell Labs (and before he moved on to MIT) Shannon published a paper called “A Mathematical Theory of Communication.”

Using probability tools developed by Norbert Wiener a decade earlier, Shannon theorized that all communication can be broken down into digital units called “bits” (for binary digits.)

He further theorized that any communication channel can handle only so much information before an accurate signal traveling over it becomes overwhelmed by noise or interference.

All later math and engineering work that helps code information at one end and accurately decode it on the receiving end of its transmission was based on Shannon’s work, El Gamal says.

That includes file compression, signal processing and analyzing human blood looking for tiny amounts of cancer DNA, as the Guardant 360 test does.


“We generate massive amounts of data” Eltouky says of a test that the company’s website covers “68 relevant genes that interrogate all active disease sites.”

The tests also take advantage of new insights into how quickly cancer cells mutate.

Those mutations can create false positives in oncology testing because the cancer DNA left in the body can be significantly distinct from that cut out in a biopsy.

“People don’t have cancer; they have cancers,” says Eltoukhy, whose last start-up, Avantome, developed low-cost genetic sequencing technology and was acquired by Illumina for $60 million in 2009.

Guardant 360 represents “a three-orders-of-magnitude improvement in specificity and sensitivity” to biopsies for lung cancer and other cancers, says Eltoukhy, who was named a “2015 Pioneer” at the World Economic Forum in Davos earlier this year.

The company plans to use a just-completed $50 million round of venture capital financing to hire roughly equal numbers of engineers and sales people, he told me during a phone interview.

There are 12 million cancer patients in the U.S.