Vancouver-based company wants to take ‘undiagnosed’ out of the medical vocabulary
Imagine if you will that whenever you get sick, doctors will be able to pin down the exact bug that’s flattening you and then will be able to identify the right drug to clobber it, first time, every time.
Imagine that air samples taken from pig farms could tell us when swine flu is in the air, and that samples from chicken farms could flag avian influenza – and would not only tell us that the flu was in the air, but the exact strain. Imagine, no more ineffective treatments because doctors couldn’t figure out which version of the pathogen was involved, so couldn’t pick the best medication, and no more mass purges of livestock because there’s no way to tell which pig or chicken is infected.
Science fiction? Not if Vancouver’s Fusion Genomics has anything to say about it. Fusion has developed a process to identify any known pathogen within about 12 hours, giving doctors the potential to take the word “undiagnosed” out of their vocabularies.
Today, one million critically ill people in the U.S. remain undiagnosed each year, and many of them spend a long time in the hospital because of it, or even die, according to Dr. Mohammed Qadir, Fusion’s president and chief scientific officer. He said the direct cost to the healthcare system is US$27 billion.
There are, he noted, over 1,400 known human pathogens, and our bodies contain more bacteria (some friendly, some not) than human cells. Current tests look for pathogens one at a time. Once you know you have, say, hepatitis, tests can tell what strain lives in you so doctors can choose the appropriate drug, but getting there can eat up time (and money) that the patient may not have.
Fusion’s test, appropriately called ONETest, does everything in one grand swoop — identify the pathogen, and strain and often even what year it first was seen, and where. (Just as we have breeds of dog, each different, there are many breeds, known as strains, of each pathogen. The reason our flu shots often don’t work is that the vaccine is science’s best guess as to which ones will show up in a given year.)
The test kit comes with a sample prep kit, and some synthetic DNA and RNA called QUANTUMProbes. First, the patient’s sample is prepared, and the pathogens extracted using the QUANTUMProbes, which bind to the infectious agents and allow them to be separated from the patient’s normal cells. Then the pathogen’s genome is sequenced through the hospital’s next generation sequencing (NGS) machine.
The final step is handing off the results of that DNA sequencing to the IBM Cloud (chosen, Dr. Qadir said, because of its ability to quickly scale up or down while ensuring that sensitive data is protected), where Fusion’s machine learning software compares it to that of all known pathogens and produces results.
Those results let the doctor make a diagnosis and get going on appropriate treatment. The entire process currently takes about 24 hours, but by the time it’s released for research use in the fourth quarter of next year, Dr. Qadir hopes to cut that time in half, and then further reduce it to around 8 hours as time goes on (what he calls “the Hollywood version” of real-time diagnosis is farther in the future). He hopes that all regulatory approvals to allow it to go mainstream will be complete by 2020.
The tests are already in clinical use, looking for upper respiratory infections.
Dr. Qadir claims that the process is up to 10,000 times more sensitive than other genomic solutions, and he ultimately wants to get the cost per test down to under one tenth of their cost. He sees it being used in many other places besides in hospitals, to identify the signs of a pandemic before it becomes severe, or to do environmental monitoring for things like swine or avian flu in the air or E.coli in drinking water.
“The power of the platform is in pre-emergence,” he said. “Our wider aim is to make it harder to have undiagnosed illnesses.”