Researchers develop fast, accurate cystic fibrosis test

February 2, 2016, Stanford University Medical Center
Researchers develop fast, accurate cystic fibrosis test
Stanford researchers have developed a method that allows them to extract DNA from tiny drops of blood — like those taken during newborn screenings — in order to look for genetic mutations that cause cystic fibrosis. Credit: Shutterstock

Researchers at the Stanford University School of Medicine have developed a fast, inexpensive and highly accurate test to screen newborns for cystic fibrosis. The new method detects virtually all mutations in the CF gene, preventing missed diagnoses that delay babies' ability to begin receiving essential treatment.

A paper describing the published online Feb. 1 in The Journal of Molecular Diagnostics. Cystic fibrosis, which causes mucus to build up in the lungs, pancreas and other organs, is the most common fatal genetic disease in the United States, affecting 30,000 people. To develop the disease, a child must inherit two mutated copies of the CF gene, one from each parent. Newborns in every U.S. state have been screened for CF since 2010, but the current tests have limitations.

"The assays in use are time-consuming and don't test the entire gene," said the study's senior author, Curt Scharfe, MD, PhD. "They don't tell the whole story." Scharfe was a senior scientist at the Stanford Genome Technology Center when the study was conducted and is now associate professor of genetics at the Yale School of Medicine.

"Cystic fibrosis has shown us that early diagnosis really matters," said Iris Schrijver, MD, a co-author of the study and professor of pathology at Stanford. Schrijver directs the Stanford Molecular Pathology Laboratory, which has a contract with California for the state's newborn CF testing.

Advantages of early diagnosis, medical attention

Prior studies have shown that newborn screening and prompt medical follow-up reduce symptoms of CF such as lung infections, airway inflammation, digestive problems and growth delays. "When the disease is caught early, physicians can prevent some of its complications, and keep the patients in better shape longer," Schrijver said. Although classic CF still limits patients' life spans, many of those who receive good medical care now live into or beyond their 40s.

In the current test, babies' blood is first screened for immunoreactive trypsinogen, an enzyme that is elevated in CF cases but also can be high for other reasons, such as in infants with one mutated copy and one normal copy of the CF gene. Since the majority of infants with high trypsinogen will not develop CF, most U.S. states follow up with genetic screening to detect mutations in the CF gene. California, which has the most comprehensive screening process, tests for 40 CF-causing mutations common in the state. (More than 2,000 mutations in the CF gene are known, though many are rare). If one of the common mutations is identified, the infant's entire CF gene is sequenced to try to confirm whether the baby has a second, less common CF mutation.

The process takes up to two weeks and can miss infants who carry two rare CF mutations, particularly in nonwhite populations about whose CF changes scientists have limited knowledge.

DNA from dried blood spots

The Stanford-developed method greatly improves the gene-sequencing portion of screening, comprehensively detecting CF-causing mutations in one step, at a lower cost and in about half the time now required. Stanford University is exploring the possibility of filing a patent for the technique.

To enable these improvements, the team developed a new way to extract and make many copies of the CF gene from a tiny sample of DNA—about 1 nanogram—from the dried blood spots that are collected on cards from babies for newborn screening. "These samples are a very limited and precious resource," Scharfe said. The entire CF gene then undergoes high-throughput sequencing. This is the first time scientists have found a way to reliably use dried for this type of sequencing for CF, which typically requires much more DNA.

"In our new assay, we are reading every letter in the book of the CF gene," Schrijver said. "Whatever mutations pop up, the technique should be able to identify. It's a very flexible approach."

In order for the new test to be adopted, the molecular pathology lab needs to train its staff on the new procedure and run thorough validation studies as part of regulatory and quality requirements to show that the reliability of the test in a research setting will be maintained in the larger-scale clinical laboratory. California newborn screening officials will then have the opportunity to decide whether they want the new test to replace the current method. Schrijver expects the process will take less than a year. "Regardless of how the state decides, the new technique can be widely adopted in different settings," she said, noting that the technique could also be used for carrier and diagnostic testing and to screen for other genetic diseases, not just CF.

"Ultimately, we would like to develop a broader assay to include the most common and most troublesome newborn conditions, and be able to do the screening much faster, more comprehensively and much more cheaply," Scharfe said.

The work is an example of Stanford Medicine's focus on precision health, the goal of which is to anticipate and prevent disease in the healthy and precisely diagnose and treat disease in the ill.

Explore further: Ethnic differences in CF genetic coding not addressed in screening tests for nonwhite patients

Related Stories

Ethnic differences in CF genetic coding not addressed in screening tests for nonwhite patients

December 16, 2015
Cystic fibrosis (CF) occurs less frequently in nonwhites than in whites, and nonwhites tend to be diagnosed at a later age. This late diagnosis often comes only once they have become symptomatic, rather than through newborn ...

Gene replacement in pigs ameliorates cystic fibrosis-associated intestinal obstruction

May 8, 2013
Cystic fibrosis (CF) is caused by mutations in CFTR and is characterized by dysfunction of the lungs, liver, pancreas, and intestines. Approximately 15% of babies with CF are born with an obstruction of the small intestine ...

Of mice and men (and pigs), a cystic fibrosis mystery solved

January 28, 2016
New research from the University of Iowa answers a question that has vexed cystic fibrosis (CF) researchers for almost 25 years: why don't mice with CF gene mutations develop the life-threatening lung disease that affects ...

Cystic fibrosis deadlier for Hispanic than non-Hispanic patients, study finds

June 24, 2015
Cystic fibrosis is more deadly for Hispanic than non-Hispanic patients, a disparity that is not explained by differences in their access to health care, according to a new study from the Stanford University School of Medicine.

Improved gene therapy is a promising candidate for cystic fibrosis treatment

November 16, 2015
An improved gene therapy treatment can cure mice with cystic fibrosis (CF). Cell cultures from CF patients, too, respond well to the treatment. Those are the encouraging results of a study presented by the Laboratory for ...

Researchers further illuminate pathway for treatment of cystic fibrosis

January 13, 2016
It is well established that people with cystic fibrosis (CF) have two faulty copies of the CFTR gene, but debate continues on the question of whether certain symptoms of the airway disease are caused by the mutation or if ...

Recommended for you

Obesity, infertility and oxidative stress in mouse egg cells

August 16, 2018
Excessive body fat is associated with negative effects on female fertility and pregnancy. In mice, maternal obesity impairs proper development of egg precursor cells called oocytes. In a recent paper published in Molecular ...

New imaging technique can spot tuberculosis infection in an hour

August 16, 2018
Guided by glowing bacteria, researchers have devised an imaging technique that can diagnose live tuberculosis in an hour and help monitor the efficacy of treatments. That's particularly critical because many TB strains have ...

Research shows it's possible to reverse damage caused by aging cells

August 15, 2018
What's the secret to aging well? University of Minnesota Medical School researchers have answered it- on a cellular level.

This matrix delivers healing stem cells to injured elderly muscles

August 15, 2018
A car accident leaves an aging patient with severe muscle injuries that won't heal. Treatment with muscle stem cells from a donor might restore damaged tissue, but doctors are unable to deliver them effectively. A new method ...

Male tobacco smokers have brain-wide reduction of CB1 receptors

August 15, 2018
Chronic, frequent tobacco smokers have a decreased number of cannabinoid CB1 receptors, the "pot receptor", when compared with non-smokers, reports a study in Biological Psychiatry.

Doctors may be able to enlist a mysterious enzyme to stop internal bleeding

August 14, 2018
Blood platelets are like the sand bags of the body. Got a cut? Platelets pile in to clog the hole and stop the bleeding.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.