Research team diagnoses asthma with nasal brush test

June 11, 2018, The Mount Sinai Hospital
Study flow for the identification of a nasal brush-based classifier of asthma by machine learning analysis of RNAseq data. One hundred and ninety subjects with mild/moderate asthma and controls without asthma were recruited for phenotyping, nasal brushing, and RNA sequencing of nasal brushings. The RNAseq data generated were then a priori split into development and test sets. The development set was used for differential expression analysis and machine learning (involving feature selection, classification, and statistical analyses of classification performance) to identify an asthma classifier that can classify asthma from no asthma as accurately as possible. The asthma classifier was then evaluated on eight test sets, including (1) the RNAseq test set of independent subjects with and without asthma, (2) two external test sets of subjects with and without asthma with nasal gene expression profiled by microarray, and (3) five external test sets of subjects with non-asthma respiratory conditions (allergic rhinitis, upper respiratory infection, cystic fibrosis, and smoking) and nasal gene expression profiled by microarray. Figure drawn by Jill Gregory, Mount Sinai Health System, licensed under CC-BY-ND. Credit: Jill Gregory, Mount Sinai Health System, licensed under CC-BY-ND

Mount Sinai researchers have identified a genetic biomarker of asthma that can be tested for using a simple nasal brush and basic follow-up data analysis. This inexpensive diagnostic test can accurately identify mild to moderate asthma and differentiate it from other respiratory conditions such as allergic rhinitis, smoking, upper respiratory infection, and cystic fibrosis. The research team, led by a collaboration of clinical and computational scientists in the Department of Genetics and Genomic Sciences, the Icahn Institute for Genomics and Multiscale Biology, and the Department of Pediatrics at the Icahn School of Medicine at Mount Sinai, published their results in June 2018 in Scientific Reports.

"Mild to moderate can be difficult to diagnose because symptoms change over time and can be complicated by other ," said Dr. Supinda Bunyavanich, physician and researcher at the Icahn School of Medicine. "Our nasal brush test takes seconds to collect—for time-strapped clinicians, particularly primary care providers at the frontlines of asthma diagnosis, this could greatly improve patient outcomes through early and accurate diagnosis."

Currently, pulmonary function testing (PFT) is the most reliable diagnostic tool for asthma. However, access to the equipment and expertise needed to perform these tests is not always prevalent in primary care settings where asthma is frequently diagnosed and treated. It is also difficult to differentiate between asthma and other respiratory diseases using PFT alone, while the nasal brush and subsequent analysis for this asthma biomarker provides a binary result of asthma or not asthma.

Data scientists leading the study applied machine learning algorithms to the genetic (RNA) data acquired from nasal brushes of patients with and without asthma. This robust data collection, and machine learning analysis identified a 90-gene biomarker indicative of asthma status. "One of the most exciting components of this study is demonstrating the power of machine learning when applied to biomedical data," said Dr. Gaurav Pandey, who led data science efforts to develop the biomarker. "Collaborations between computational scientists and biomedical researchers and clinicians are advancing medicine at an inspiring pace—we have the power of insights we didn't have many of in the past and that opens a window to an entirely new world of diagnostic tools and treatments"

Similar genetic biomarker tests are currently being used in other disease areas, including MammaPrint and Oncotype DX, both used for certain types of . In fact, the Oncotype DX tool was used in the largest clinical trial of personalized breast cancer prognosis ever conducted, demonstrating that mammography testing is unnecessary to diagnose breast cancer in a large fraction of breast cancer patients. The positive clinical impact biomarker tests such as this have shown indicate great potential for further diagnostic tools based on biomarkers.

Dr. Bunyavanich says the next step to bringing this test into clinical practice is a study in a larger population of patients. "With prospective validation in large cohorts, our asthma could lead to the development of a minimally invasive test to aid asthma diagnosis at clinical frontlines where time and resources often preclude pulmonary function testing."

Asthma affects 10 percent of children and adults in the United States. When undiagnosed, it can lead to restricted activity, emergency room visits, and hospitalizations. "We're hopeful that further studies can help bring this into primary care settings, transforming the ease and accuracy of diagnosing asthma and our ability as doctors to appropriately treat our patients," said Dr. Bunyavanich.

Explore further: Researchers identify common biological features of different types of asthma

More information: Gaurav Pandey et al, A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data, Scientific Reports (2018). DOI: 10.1038/s41598-018-27189-4

Related Stories

Researchers identify common biological features of different types of asthma

March 14, 2018
A team of researchers from the NIHR Leicester Biomedical Research Centre - a partnership between Leicester's Hospitals, the University of Leicester and Loughborough University - has identified biological variations in lung ...

Raising awareness about asthma is critical, says expert

May 15, 2018
Millions of people in the United States, regardless of age, gender, race and ethnicity, are impacted by asthma, and the number of asthma sufferers is only projected to grow. To raise awareness about this disease, May is recognized ...

Asthma management tools improve asthma control and reduce hospital visits

March 13, 2018
A set of comprehensive asthma management tools helps decrease asthma-related visits to the emergency department, urgent care or hospital and improves patients' asthma control.

Serum periostin IDs comorbid chronic rhinosinusitis in asthma

March 21, 2017
(HealthDay)—For patients with asthma, serum periostin is useful for detecting chronic rhinosinusitis with nasal polyps, according to a study published online March 1 in the Annals of the American Thoracic Society.

Maternal uncontrolled asthma ups risk of asthma in offspring

July 17, 2017
(HealthDay)—Children whose mothers have uncontrolled asthma during pregnancy are at increased risk of developing the disease at a young age, according to a study published online July 13 in the Journal of Allergy and Clinical ...

Test used to diagnose asthma may not be accurate

December 5, 2016
A new study urges caution in the use of the mannitol challenge test for asthma in non-clinical settings. The test is considered widely applicable to detect asthma, but its accuracy outside of patients referred for specialized ...

Recommended for you

Sugar, a 'sweet' tool to understand brain injuries

October 15, 2018
Australian researchers have developed ground-breaking new technology which could prove crucial in treating brain injuries and have multiple other applications, including testing the success of cancer therapies.

Scientists reveal new cystic fibrosis treatments work best in inflamed airways

October 11, 2018
A new UNC School of Medicine study shows that two cystic fibrosis (CF) drugs aimed at correcting the defected CFTR protein seem to be more effective when a patient's airway is inflamed. This is the first study to evaluate ...

Microbiome profiling reveals associations with ulcerative colitis severity, treatment

October 11, 2018
A study of gut microbes from more than 400 children points to how the microbiome behaves in this inflammatory bowel disease.

Genomic study finds a new role for microRNAs as predictors of Crohn's disease progression

October 4, 2018
Crohn's disease is a lifelong condition characterized by a fluctuating course of gastro-intestinal inflammation with repeated flares and remissions. Any part of the alimentary tract from the mouth to the anus can be affected ...

Immune system's balancing act keeps bowel disease in check

October 2, 2018
Australian researchers have uncovered clues in the immune system that reveal how the balance of 'good' gut bacteria is maintained. The information could help in the prevention and treatment of inflammatory bowel disease (IBD).

Single cell analysis paves the way for better treatments for IBD

October 2, 2018
Researchers at MRC HIU examined the large intestine using sophisticated single cell technology, in work that paves the way for better treatments for IBD.

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.