Giulia KennedyPhD
VeracyteChapter 11 · Strand B · Achievement

A patent family

Co-inventor on more than 20 patents. The Veracyte family runs from a 2009 priority date on molecular profiling of thyroid nodules to grants in 2024 and 2025, with separate lines on sample classification and detecting usual interstitial pneumonia.

OCT 2019 – MAY 2025CO-INVENTORVERACYTE, INC. · SOUTH SAN FRANCISCO, CALIFORNIA

Overview

Veracyte’s biography of Kennedy describes her as a co-inventor on more than 20 patents, a figure the Acuamark board announcement repeated in 2023.12 The research behind this site confirmed her inventorship on eleven granted US patents across the Affymetrix and Veracyte years; the Veracyte family is gathered here. The marker sits at the October 2019 grant of US 10,446,272; the family’s earliest priority date is May 7, 2009.

The thyroid molecular-profiling family

The core line begins with two applications from 2009. US 8,669,057, “Methods and compositions for diagnosis of thyroid conditions”, carries a priority date of May 7, 2009 and was granted on March 11, 2014; US 8,541,170, “Methods and compositions of molecular profiling for disease diagnostics”, was filed on November 17, 2009.34 Both name the same eight inventors: Giulia C. Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee and Jonathan I. Wilde. The same group appears on the continuations that followed a decade later: US 12,110,554, “Methods for classification of tissue samples as positive or negative for cancer”, issued October 8, 2024; US 12,297,503, granted May 13, 2025; and US 12,305,238, “Methods for treatment of thyroid cancer”, issued May 20, 2025 with continuations reaching back to 2017.567 US 9,856,537, “Algorithms for disease diagnostics”, names Kennedy with Chudova, Wang and Wilde.8

Sample classification and the lung

A separate line, US 10,446,272, “Methods and compositions for classification of samples”, filed September 12, 2017 and granted October 15, 2019, covers methods for classifying samples, including identifying sample mix-ups.9 The Envisia work produced its own patents: US 11,639,527, “Methods for nucleic acid sequencing”, granted May 2, 2023, and US 11,976,329, “Methods and systems for detecting usual interstitial pneumonia”, granted May 7, 2024 from a provisional filed in September 2016.1011

Earlier Affymetrix-era patents on genotyping are recorded in the whole-genome genotyping chapter.

From the record

Facts

  • Veracyte's biography describes Kennedy as a co-inventor on more than 20 patents; the Acuamark board announcement in 2023 repeats the figure.12
  • Named inventor on US 8,541,170, "Methods and compositions of molecular profiling for disease diagnostics", filed November 17, 2009 and assigned to Veracyte.4
  • Named inventor on US 8,669,057, "Methods and compositions for diagnosis of thyroid conditions", priority date May 7, 2009, granted March 11, 2014.3
  • Named inventor on US 9,856,537, "Algorithms for disease diagnostics", with Darya I. Chudova, Eric T. Wang and Jonathan I. Wilde, assigned to Veracyte.8
  • Named inventor on US 10,446,272, "Methods and compositions for classification of samples", filed September 12, 2017 and granted October 15, 2019.9
  • Named inventor on US 12,110,554, "Methods for classification of tissue samples as positive or negative for cancer", issued October 8, 2024 as a continuation in the thyroid molecular-profiling family.5
  • Named inventor on US 12,297,503, filed September 3, 2024 and granted May 13, 2025, relating to molecular profiles associated with thyroid cancer.126
  • Named inventor on US 12,305,238, "Methods for treatment of thyroid cancer", filed September 23, 2024 and issued May 20, 2025.7
  • Named inventor on two Envisia-related patents: US 11,639,527, "Methods for nucleic acid sequencing" (granted May 2, 2023), and US 11,976,329, "Methods and systems for detecting usual interstitial pneumonia" (granted May 7, 2024).1011

Contributions

  • Co-inventor, with Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee and Jonathan I. Wilde, on the thyroid molecular-profiling patent family that underlies Afirma.435

Research

  • Thyroid nodule genomic classification

    APR 2008 – DEC 2022

    The programme that defined Veracyte, where Kennedy was Chief Scientific Officer from 2008 and Chief Medical Officer from 2018. The Afirma Gene Expression Classifier was developed from 315 nodules (JCEM, 2010), launched in January 2011 and validated prospectively in 3,789 patients (NEJM, 2012). The RNA sequencing-based Afirma GSC followed in 2017, validated in JAMA Surgery (2018) with at least one third more benign calls than the original test, and was extended with the Xpression Atlas of variants and fusions, Hürthle cell and medullary thyroid carcinoma classifiers. By January 2018 Veracyte had performed 100,000 Afirma tests.

  • 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
  • Afirma Gene Expression Classifier
  • Afirma Genomic Sequencing Classifier
  • Envisia Genomic Classifier

Achievements

  1. 17 NOV 2009patent

    US 8,541,170: Methods and compositions of molecular profiling for disease diagnostics

    Application US12/592,065, filed November 17, 2009 and assigned to Veracyte; inventors Giulia C. Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee and Jonathan I. Wilde. Dated here by filing; the grant date in the research snippet needs confirmation on the patent face.4

  2. 11 MAR 2014patent

    US 8,669,057: Methods and compositions for diagnosis of thyroid conditions

    Granted March 11, 2014 with a priority date of May 7, 2009; assigned to Veracyte. Inventors Giulia C. Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee and Jonathan I. Wilde.3

  3. 15 OCT 2019patent

    US 10,446,272: Methods and compositions for classification of samples

    Filed September 12, 2017 and granted October 15, 2019 to Veracyte; inventors Jonathan I. Wilde, Darya Chudova and Giulia C. Kennedy. Covers methods for classifying samples, including detecting sample mix-ups.9

  4. 2 MAY 2023patent

    US 11,639,527: Methods for nucleic acid sequencing

    Granted May 2, 2023 to Veracyte; covers sequencing and analysis of nucleic acids to determine that a subject is positive for a non-usual interstitial pneumonia subtype. Inventors include Giulia C. Kennedy, Daniel Pankratz, Su Yeon Kim, Yoonha Choi, Jing Huang and Moraima Pagan.10

  5. 7 MAY 2024patent

    US 11,976,329: Methods and systems for detecting usual interstitial pneumonia

    Granted May 7, 2024 to Veracyte, with an earliest provisional application of September 7, 2016; inventors Giulia C. Kennedy, Jing Huang, Yoonha Choi, Daniel Pankratz and Patric Sean Walsh.11

  6. 8 OCT 2024patent

    US 12,110,554: Methods for classification of tissue samples as positive or negative for cancer

    Issued October 8, 2024 to Veracyte on application 17/157,876, a continuation in the thyroid molecular-profiling family; inventors Giulia C. Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee and Jonathan I. Wilde.5

  7. 13 MAY 2025patent

    US 12,297,503: molecular profiles associated with thyroid cancer

    Filed September 3, 2024 and granted May 13, 2025 to Veracyte; relates to molecular profiling and cancer diagnostics, in particular molecular profiles associated with thyroid cancer. Inventors include Giulia C. Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee and Jonathan I. Wilde. The full title was not captured by the research.126

  8. 20 MAY 2025patent

    US 12,305,238: Methods for treatment of thyroid cancer

    Filed September 23, 2024 as application 18/893,597 and issued May 20, 2025 to Veracyte, with continuations dating back to 2017; inventors Giulia C. Kennedy, Darya I. Chudova, Eric T. Wang, Jonathan I. Wilde, Bonnie H. Anderson, Hui Wang, Moraima Pagan and Nusrat Rabbee.7

Impact

  • US 8,541,170: METHODS AND COMPOSITIONS OF MOLECULAR PROFILING FOR DISEASE DIAGNOSTICS

    Foundational member of the Afirma thyroid molecular-profiling patent family.

  • US 11,976,329: METHODS AND SYSTEMS FOR DETECTING USUAL INTERSTITIAL PNEUMONIA

    Patent protection for the Envisia approach to detecting UIP.

Impact across the career