2021
DOI: 10.1016/j.chest.2021.08.026
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Abstract: Accurate assessment of the risk of malignancy (ROM) is critical in the management of a screen-detected or incidental pulmonary nodule (PN) to minimize procedures for benign disease and for timely diagnosis and treatment of patients with lung cancer. We recently demonstrated that a clinical-genomic classifier using RNA whole-transcriptome sequencing of cells from the nasal epithelium in ever-smokers with a PN can accurately classify cancer risk. 1 Now unblinded after clinical validation, we show that the classi… Show more

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Cited by 2 publications
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“…The Unified Assay was used to generate RNA-Seq data from deidentified clinical samples collected during the development and implementation of the aforementioned tests [ 12 , 13 , 14 , 16 , 22 , 24 , 25 , 27 , 28 , 29 , 43 , 44 , 45 ] and processed through the CLIA-certified laboratory. The RNA exome biorepository described herein is comprised of 120,312 clinical samples across 3 major clinical indications, where each clinical sample was processed and sequenced for 26,268 genes ( Table 1 ).…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…The Unified Assay was used to generate RNA-Seq data from deidentified clinical samples collected during the development and implementation of the aforementioned tests [ 12 , 13 , 14 , 16 , 22 , 24 , 25 , 27 , 28 , 29 , 43 , 44 , 45 ] and processed through the CLIA-certified laboratory. The RNA exome biorepository described herein is comprised of 120,312 clinical samples across 3 major clinical indications, where each clinical sample was processed and sequenced for 26,268 genes ( Table 1 ).…”
Section: Resultsmentioning
confidence: 99%
“…Sequencing data were analyzed via the following advanced machine learning-based classifiers (all developed/licensed by Veracyte, Inc., South San Francisco, CA, USA) that are applied to the diagnosis of thyroid cancer, interstitial lung disease (ILD), and lung cancer, and may be applicable to other disease indications: the Afirma ® Genomic Sequencing Classifier (GSC), which uses RNA exome sequencing information derived from a fine-needle aspiration (FNA) biopsy to classify cytologically indeterminate thyroid nodules as Afirma GSC Benign or Suspicious [ 12 , 22 , 23 , 24 , 25 ]; the Afirma Xpression Atlas (XA), which provides genomic alteration information from FNA samples with an Afirma GSC Suspicious result, or cytologically suspicious for malignancy or malignancy nodule [ 26 ]; the Envisia ® Genomic Classifier (GC), a diagnostic test that uses a 190-gene expression signature to differentiate between usual interstitial pneumonia (UIP) and non-UIP subtypes in lung transbronchial biopsy (TBB) samples from patients with ILD [ 13 ]; the Percepta GSC, which uses RNA exome sequencing information from bronchial brushing samples for classification of lung cancer risk among bronchoscopy nondiagnostic samples [ 16 ]; the Percepta Nasal Swab (NS) classifier that uses RNA exome sequencing information from nasal (inferior turbinate) samples to classify the risk of lung cancer in patients with previously detected lung nodules [ 27 ]; and the Percepta Genomic Atlas (GA) test, which was developed to detect lung cancer-associated fusions and MET exon-skipping events in diagnostic TBB specimens and transbronchial needle aspirates (TBNAs) [ 28 ]. Beyond expression signatures, interrogation of RNA-Seq data in these samples revealed specimens with rare and novel genomic events, including gene fusions, mitochondrial variants, and loss of heterozygosity (LOH).…”
Section: Methodsmentioning
confidence: 99%
“…The data presented in the abstract was promising with high low-risk and high-risk sensitivity and specificity, respectfully. In addition, the authors further updated the clinical validation performance to be inclusive of prior cancers [22]. By having two decision boundaries, high and low-cut offs, the investigators were able to move more patients from intermediate to either low risk or high-risk categories.…”
Section: Percepta Nasal Swab Classifiermentioning
confidence: 99%