Weill Cornell's precision cancer test ready for clinical use

Scientists say EXaCT-1 has proven to be reliable and reproducible.
By Bernie Monegain
10:40 AM

Scientists at Weill Cornell Medicine say EXaCT-1, the new genome sequencing test to detect mutations, can guide precision cancer treatment with more than 95 percent accuracy.

Their findings were published July 20 in the journal npj Genomic Medicine. The results confirm the feasibility of Weill Cornell Medicine EXaCT-1, in a clinical setting, the scientists say.

EXaCT-1 scans 21,000 genes to detect genetic mutations that drive cancer.  The information helps researchers find new treatments and clinical trials.

"We had to demonstrate that we can do genomic testing reliably and reproducibly and that we have procedures in place that are robust and compatible with clinical testing," said co-senior author Olivier Elemento, who heads the Englander Institute's computational biology group, and serves as associate professor of physiology and biophysics and associate director of the Institute for Computational Biomedicine at Weill Cornell Medicine.

[Also: Vice President Biden announces vast list of federal and private-sector collaborations at Cancer Moonshot Summit]

To make sure the EXaCT-1 is reliable and reproducible, researchers tested its algorithm, based on a type of test known as whole exome sequencing, on 57 tumors for any mutation in five genes.

"We worked hard to show that the test is reliable and can find mutations that exist while also not falsely find mutations that don't exist," Elemento said in a statement.

Elemento's team developed a suite of analytic tools that analyzes the data, detects mutations, generates a physical report for physicians to review with their advanced cancer patients and stores the report automatically within the electronic health record.

The entire process takes about three weeks on average, the researchers say, but they have also shown that it is feasible to perform the test in just six days.

[Also: Intermountain, Stanford, others launch data sharing network for Biden’s Cancer Moonshot]

The test has identified expected mutations, or those associated with a specific treatment protocol, as well as potentially relevant mutations in 82 percent of cases involving 337 patients.

While EXaCT-1 is primarily an oncology test, researchers can also use it to determine how responsive a patient would be to immunotherapy or to obtain information about a patient's inherited genome, known as the germline.

Last fall, EXaCT-1 became the first whole exome test to be approved by the New York State Department of Health for oncology testing.

"That was no easy feat," said co-senior author Mark Rubin.

"The rigorous nature of the development, testing and validation makes it a challenge for most groups to get approval," said Rubin, director of the Englander Institute and professor of oncology in pathology at Weill Cornell Medicine. Rubin also heads the precision medicine program at Weill Cornell Medicine and NewYork-Presbyterian/Weill Cornell Medical Center."

Twitter: @Bernie_HITN
Email the writer: bernie.monegain@himssmedia.com

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