Evidence map›Paper›PMID 40165118›Full record

ArticleBMC cancer2025

Analytical validation of the Percepta Nasal Swab classifier; an RNA next-generation sequencing assay for the assessment of lung cancer risk in pulmonary nodules.

Shuyang Wu, Ruochen Jiang, Grazyna Fedorowicz, Mei Wong, Janna S Chamberlin, Lori Lofaro, P Sean Walsh, Giulia C Kennedy, Yangyang Hao, Jing Huang and 1 more

Abstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC cancer, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Shuyang WuVeracyte, Inc., South San Francisco, CA, 94080, USA.
Ruochen JiangVeracyte, Inc., South San Francisco, CA, 94080, USA.
Grazyna FedorowiczVeracyte, Inc., South San Francisco, CA, 94080, USA.
Mei WongVeracyte, Inc., South San Francisco, CA, 94080, USA.
Janna S ChamberlinVeracyte, Inc., South San Francisco, CA, 94080, USA.
Lori LofaroVeracyte, Inc., South San Francisco, CA, 94080, USA.
P Sean WalshVeracyte, Inc., South San Francisco, CA, 94080, USA.
Giulia C KennedyVeracyte, Inc., South San Francisco, CA, 94080, USA.
Yangyang HaoVeracyte, Inc., South San Francisco, CA, 94080, USA.
Jing HuangVeracyte, Inc., South San Francisco, CA, 94080, USA.
Bill BulmanVeracyte, Inc., South San Francisco, CA, 94080, USA. bill.bulman@veracyte.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundA novel molecular diagnostic test, Percepta Nasal Swab (PNS), was developed as a noninvasive lung cancer biomarker to aid in risk assessment for indeterminate pulmonary nodules in individuals who smoke or have previously smoked. Prior research has shown that exposure of the airway epithelium to cigarette smoke results in epithelial gene expression alterations throughout the respiratory tree that reflect the risk of lung cancer in a pulmonary nodule. The PNS classifier leverages this concept using whole transcriptome sequencing (RNASeq) of cells collected from the nasal epithelium and provides "high", "intermediate" and "low risk" classification calls to help guide clinical management decisions. The clinical validity of the PNS test was established on an independent validation set and demonstrated favorable sensitivity and specificity. This study aims to evaluate the analytical validity of the PNS test performance in our CLIA (Clinical Laboratory Improvement Amendments) laboratory.

methodsThe reproducibility between RNASeq runs within a laboratory and the accuracy between laboratories were estimated and compared against the performance-based acceptance criterion. The impacts from varying RNA input amount, genomic DNA and blood RNA interference were evaluated to demonstrate the analytical sensitivity and specificity of the PNS test results to known conditions that may occur in routine laboratory processing.

resultsBased on modeling the impact on clinical sensitivity/specificity, PNS test classifier scores can allow up to 0.776 score units of added noise/variability before any performance metrics drop below the pre-specified requirements. This allowable variability is six-fold higher than the observed variability estimated between runs and between laboratories under routine testing conditions, which are each less than 2% of the 98th percentile score range. In addition, PNS test results are shown to be robust against RNA input variation from 50 ng to 15 ng, up to 30% of genomic DNA by nucleic mass interference, and up to 14% of blood RNA interference.

conclusionsThis study provided sufficient evidence for the accuracy, reproducibility, sensitivity, and specificity of the PNS molecular test and supported its utilization in clinical testing.

Indexed as

Biomarkers, TumorHigh-Throughput Nucleotide SequencingLung NeoplasmsMultiple Pulmonary NodulesNasal MucosaFemaleHumansMaleMiddle AgedReproducibility of ResultsRisk AssessmentSensitivity and SpecificityBiomarkers, TumorAnalytical validationGenomicsLung cancer riskMolecular diagnostic testNasal Swab classifierPulmonary nodules

Identifiers

PMID40165118
PMCPMC11960024

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.