Giulia KennedyPhD
VeracyteChapter 09 · Strand B · Research

Percepta and Envisia

Genomic classifiers for the lung: Percepta for suspicious nodules after an inconclusive bronchoscopy (2015), Envisia for idiopathic pulmonary fibrosis without surgical biopsy (2016), and a nasal swab test for lung cancer risk.

APR 2015 – APR 2024CHIEF SCIENTIFIC OFFICER AND CHIEF MEDICAL OFFICER, VERACYTEVERACYTE, INC. · SOUTH SAN FRANCISCO, CALIFORNIA

Overview

After Afirma, Veracyte turned the same approach to the lung. Two clinical questions were chosen because the existing answer was an invasive procedure: whether a suspicious lung nodule is cancer when bronchoscopy is inconclusive, and whether a patient with interstitial lung disease has the usual interstitial pneumonia pattern that defines idiopathic pulmonary fibrosis, a diagnosis that otherwise often required surgical lung biopsy.

Contributions

Veracyte initiated the launch of the Percepta Bronchial Genomic Classifier on April 16, 2015.1 Kennedy’s authorship in the Percepta programme is on the analytical performance paper (BMC Cancer, 2016), the RNA sequencing-based Percepta Genomic Sequencing Classifier that became available to physicians on June 26, 2019 (BMC Medical Genomics, 2020), and the nasal swab classifier validated in Chest in 2024.2 When pivotal nasal swab data were announced on May 19, 2021 she said that doctors would be able to tell patients with suspicious nodules “that they are low risk for cancer and can likely avoid further work-up, with very high certainty that they have not missed a cancer”.3

Envisia was launched at the CHEST Annual Meeting on October 25, 2016, where Kennedy presented clinical validity data to pulmonologists at a private event.45 The classifier detects the UIP pattern in conventional transbronchial biopsies using RNA sequencing and machine learning. She is a co-author of the development work (Lancet Respiratory Medicine 2015, Annals of the American Thoracic Society 2017, BMC Genomics 2018), of the prospective validation study in The Lancet Respiratory Medicine in 2019, and of the 2021 AJRCCM study placing the classifier alongside high-resolution CT.67

Impact

Envisia received a final Medicare coverage policy through the MolDX program on March 4, 2019, effective April 1 that year.8 For laboratory-developed tests such as these, coverage rather than FDA clearance was the gate to clinical use. Veracyte’s biography of Kennedy counts Percepta and Envisia with Afirma as the three commercialized tests developed under her oversight.9

From the record

Facts

  • Veracyte initiated the launch of the Percepta Bronchial Genomic Classifier for lung cancer diagnosis on April 16, 2015.1
  • Veracyte launched the Envisia Genomic Classifier for idiopathic pulmonary fibrosis at the CHEST Annual Meeting on October 25, 2016; Kennedy presented clinical validity data at a private event for pulmonologists at the meeting.45
  • Envisia received a final Medicare coverage policy through Palmetto GBA's MolDX program on March 4, 2019, effective April 1, 2019.8
  • Kennedy was an author of the prospective Envisia validation study published in The Lancet Respiratory Medicine in 2019.6
  • The next-generation Percepta Genomic Sequencing Classifier became available to physicians on June 26, 2019.2
  • She authored the 2021 American Journal of Respiratory and Critical Care Medicine study of the Envisia classifier as a complement to high-resolution CT, announced July 30, 2020.7
  • On May 19, 2021 Veracyte announced pivotal validation data for the Percepta Nasal Swab test for lung cancer risk, with Kennedy quoted as chief scientific officer and chief medical officer.3

Contributions

  • Credited by Veracyte with overseeing the development of Percepta and Envisia, its second and third commercialized genomic tests.9
  • An author of the Envisia validation studies published in The Lancet Respiratory Medicine (2019) and the American Journal of Respiratory and Critical Care Medicine (2021).67

Research

  • Pulmonary genomic classifiers

    APR 2015 – APR 2024

    Veracyte's second and third commercial tests took the thyroid approach to the lung. Percepta, launched April 16, 2015, classifies lung nodules that are inconclusive by bronchoscopy from bronchial brushings; Envisia, launched October 25, 2016, identifies the usual interstitial pneumonia pattern of idiopathic pulmonary fibrosis in transbronchial biopsies without surgical lung biopsy, and received Medicare coverage effective April 1, 2019. Kennedy is an author of the Envisia development and validation papers (Annals ATS 2017, BMC Genomics 2018, Lancet Respiratory Medicine 2019, AJRCCM 2021), the Percepta analytical and GSC papers, and the 2024 Chest validation of the Percepta Nasal Swab.

  • Machine learning for clinical diagnostics

    DEC 2010 – PRESENT

    The method that links every classifier Kennedy has helped build since 2010: training algorithms on high-dimensional genomic data from clinical samples and validating them against histopathology. She presented on Veracyte's use of machine learning to translate genomic data into commercial diagnostic tests at the Precision Medicine World Conference in January 2018, and described the Afirma GSC's ensemble machine learning algorithms as deriving "from years of thoughtful scientific research, data analysis and statistical modeling". The same approach underlies the Envisia and Percepta classifiers and PinkDx's whole-transcriptome vaginal swab test.

Technologies
  • Percepta Bronchial Genomic Classifier
  • Envisia Genomic Classifier
  • Whole-transcriptome RNA sequencing
  • Ensemble machine learning classifiers

Publications

Achievements

  1. 4 MAR 2019regulatory

    Medicare coverage for the Envisia Genomic Classifier

    Veracyte received a final Medicare local coverage determination for the Envisia Genomic Classifier through Palmetto GBA's MolDX program, effective April 1, 2019.8

Impact

  • MEDICARE COVERAGE FOR THE ENVISIA GENOMIC CLASSIFIER

    Reimbursement, rather than FDA clearance, was the key gate for Veracyte's laboratory-developed tests.

Impact across the career