A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data

Sci Rep. 2018 Jun 11;8(1):8826. doi: 10.1038/s41598-018-27189-4.

Abstract

Asthma is a common, under-diagnosed disease affecting all ages. We sought to identify a nasal brush-based classifier of mild/moderate asthma. 190 subjects with mild/moderate asthma and controls underwent nasal brushing and RNA sequencing of nasal samples. A machine learning-based pipeline identified an asthma classifier consisting of 90 genes interpreted via an L2-regularized logistic regression classification model. This classifier performed with strong predictive value and sensitivity across eight test sets, including (1) a test set of independent asthmatic and control subjects profiled by RNA sequencing (positive and negative predictive values of 1.00 and 0.96, respectively; AUC of 0.994), (2) two independent case-control cohorts of asthma profiled by microarray, and (3) five cohorts with other respiratory conditions (allergic rhinitis, upper respiratory infection, cystic fibrosis, smoking), where the classifier had a low to zero misclassification rate. Following validation in large, prospective cohorts, this classifier could be developed into a nasal biomarker of asthma.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Asthma / classification
  • Asthma / diagnosis*
  • Asthma / pathology*
  • Female
  • Gene Expression Profiling*
  • Humans
  • Machine Learning*
  • Male
  • Molecular Diagnostic Techniques / methods*
  • Nasal Mucosa / pathology*
  • Predictive Value of Tests
  • Prospective Studies
  • Sensitivity and Specificity
  • Sequence Analysis, RNA*
  • Young Adult