Early candidate nasal swab classifiers developed using machine learning and whole transcriptome sequencing may improve early lung cancer detection.
Authors: Mazzone Peter J. , Lamb Carla , Rieger-Christ Kimberly M. , Reddy Chakravarthy B. , Qu Jianghan , Wu Shuyang , Ding Jie , Whitney Duncan , Pankratz Daniel G. , Babiarz Joshua , Lofaro Lori , Walsh P. Sean , Wilde Jonathon , Bhorade Sangeeta Maruti , Huang Jing , Kennedy Giulia , Spira Avrum 
Published: June 2021

8551

Background: The goal of lung nodule management is to make an early diagnosis in patients with lung cancer while avoiding unnecessary, costly and potentially harmful procedures in patients with benign lesions. Increased implementation of low dose CT screening will lead to increased numbers of both benign and malignant nodules that will require effective management. We have previously described the feasibility of detecting gene expression changes associated with lung cancer (“field of injury”) in nasal epithelium utilizing whole transcriptome RNA sequencing from non-invasive nasal brush samples. Using this approach, we now report the performance of candidate nasal classifiers that combine both genomic and clinical features to risk stratify lung nodules from ever-smokers to aid in the diagnosis of lung cancer. Methods: Patients from several clinical cohorts who were ever-smokers with a lung nodule < 30 mm and without a history of prior cancer underwent nasal epithelium sampling. All patients had at least one year of follow up or until a final diagnosis of benign or malignant nodule was made. Candidate classifiers were developed using whole-transcriptome RNA sequencing and machine learning. Training of these classifiers included genomic and clinical information (age, sex, pack-years, years-since-quit, nodule size and nodule spiculation). Two decision boundaries were chosen to maximize sensitivity and specificity for low and high-risk nodules, respectively. The performance of these classifiers was evaluated using cross-validation (CV). Results: All candidate nasal classifiers underwent CV assessment on over 700 patients with lung nodules. All candidate classifiers achieved CV performance of > 40% specificity at 95% sensitivity in low- risk nodules and all candidate classifiers achieved CV performance of > 60% sensitivity at 90% specificity in high-risk nodules. The classifiers stratified benign nodules as low- risk with > 95% negative predictive value (NPV), intermediate risk nodules were stratified as 5-65% risk and malignant nodules were stratified as high- risk with > 65% positive predictive value (PPV) in a population with estimated 25% prevalence. This performance was robust across subgroups of age ( < 65 year vs. >65 year), sex, and current versus former smokers. Conclusions: The nasal genomic-clinical candidate classifiers have a high NPV effectively identifying benign nodules when calling them low- risk, thereby, informing decisions to more safely avoid a diagnostic workup. Additionally, the high PPV of these classifiers identifies malignant nodules when calling them high- risk and informs decisions regarding the urgency of a further diagnostic work-up. A nasal genomic-clinical classifier has the potential to serve as a non-invasive tool for lung cancer risk-stratification to help inform decision making in patients with lung nodules.