New Low-Cost Test For Cystic Fibrosis

A classic sign of cystic fibrosis is excess mucus in the lungs, which makes breathing difficult and can also cause lung damage.  (iStock)

The bad news came on Kirsten McGowan's birthday. She was pregnant with her first child Patrick, and discovered she was a carrier for cystic fibrosis.

A child can only inherit the disease if both parents are carriers, and McGowan's husband also tested positive.

"It hit us out of the blue," McGowan says.

The genetic disease causes mucus to build up in the lungs and digestive system. Digestive enzymes are blocked, which inhibits the absorption of food nutrients. It's a chronic illness that can't be cured, but can be treated.

When Patrick was born with the illness, doctors put him on a diet high in protein, fat and salt so he'd maintain a healthy weight. And they outlined a daily breathing regime of two to three hours to prevent mucus build-up in his lungs.

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cystic fibrosis imageMucus builds up because CF makes it more thick and viscous.

The CF gene controls the movement of chloride ions in and out of cells, which regulates the salt and water balances in the lungs and pancreas. Mutations in this gene rob mucus of water and it builds up in the lungs it can inhibit breathing.

McGowan says detecting the illness early in Patrick meant he could get treatment right away.

"Getting a diagnosis early is key," says McGowan. "Knowing sooner helps you process that emotion--to be angry, to be sad--and then say, 'OK, now how do I help my son or daughter stay healthy."

CF is the most common fatal genetic disease in the United States. It takes just two CF gene mutation to cause cystic fibrosis and more than 2,000 changes are known.

A Rapid and Affordable New Test

Forty different genetic mutations account for most types of cystic fibrosis in California. The state tests for these common mutations but there are more than 2,000 possible changes, and more are discovered each year.

"Current tests are not comprehensive," says Stanford geneticist Curt Scharfe. "They can miss newborns with two rare mutations."

Scharfe compares the CF gene mutations to typos in a novel. But imagine a really big novel, like "War and Peace," with really unusual typos.

"Imagine changes in a letter in a word somewhere in a book," says Scharfe. "It doesn't help if you read one page very well, you need to read all these pages--or genetic changes--well. We're talking about rare typos and they happen once, not many times."

Currently, the state has a tiered testing method for CF; it tests once for common mutations and send all positive results to Stanford for further testing. Stanford does about 9,000 tests a year.

Now, researchers at Stanford have figured out how to do one test for CF using genome sequencing. The scientists were able to sequence the entire CF gene which means they can spot any and all abnormalities.

Stanford researchers were able to take enough DNA from dried blood spots to test newborns for cystic fibrosis.
Stanford researchers were able to take enough DNA from dried blood to sequence the CF gene for cystic fibrosis. (Eric T. Sheler/US Air Force)

At birth, all infants get a heel pin-prick to test their blood for a range of diseases. Stanford researchers used blood from the test to map the CF gene. Now when they test babies, the results show whether or not a baby has a mutation on that gene.

The other benefit of Stanford's new test is that researchers can sequence DNA from nearly 100 babies at once in an Illumina genome sequencing machine.

This process takes only a few days and Scharfe hopes eventually it will only take a few hours. Current tests take longer than a week.

And because the process sequences the entire CF genome it won't miss mutations, even if they are extremely rare.

The Future for Stanford's CF Test

Stanford's new test is about one-fifth the cost of current CF tests. That's partially because genome sequencing has become much less expensive. Analyzing the CF gene is possible in a way that it wasn't fifty years ago.

At age six, Patrick McGowan is extremely active and shows few outward signs of cystic fibrosis.
At age six, Patrick McGowan is extremely active and shows few outward signs of cystic fibrosis. (Kirsten McGowan)

So Scharfe hopes that, eventually, the test will be used throughout the country.

"California has the most comprehensive cystic fibrosis testing program and it would be very beneficial to have this new test available in many states."

Before California's statewide newborn screening program started in 1966, many kids with genetic disorders would go undiagnosed and symptoms would show up later.

But this hasn't been a problem for Kirsten's son Patrick.

"Outwardly he looks like any other kid walking down the sidewalk," says McGowan.

She said early detection of genetic diseases is crucial.

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"The sooner you get that news, the sooner you stop thinking ‘what if’. And then can get to that good place of living with the disease."

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