Bibliography

Giulia Kennedy, Ph.D., Co-Founder and Chief Scientific Officer. Dr. Kennedy is a molecular biologist and diagnostics innovator with deep expertise in genomics, bioinformatics and translational research.

PinkDx Scientific Breakthrough Featured on Good Morning America — PinkDx

PROspective ACcrual To Investigate reprOductive Cancers in womeN

Surgical Sample Collection- Sampling During Uterine Surgery

US8679758B2 is titled "Complexity management of genomic DNA" and lists inventors including Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, and Rui Mei, with Affymetrix Inc as the assignee.

The patent US9856537B2 "Algorithms for disease diagnostics" has inventors including Giulia C. Kennedy, Darya I. Chudova, Eric T. Wang, and Jonathan I. Wilde, and it is assigned to Veracyte Inc.

As an inventor, Dr. Kennedy has published more than 70 peer-reviewed scientific articles and is a co-inventor on more than 20 patents. Prior to Veracyte, Dr. Kennedy led the Genomics Collaborations and Genotyping Technology R&D groups at Affymetrix, Inc. Before that, she was a scientific leader for the colon cancer and breast cancer gene discovery efforts at Chiron Corporation, resulting in the identification of oncology markers for therapeutic drug development. Dr. Kennedy was previously a scientist at Millennium Pharmaceuticals, where she implemented genomic and genetic approaches to uncover diabetes susceptibility genes. She holds a Ph.D. degree in biochemistry, and completed postdoctoral training at the University of California at San Francisco in the Biochemistry Department and Hormone Research Institute.

The article was published in Proceedings of the National Academy of Sciences on December 1, 1992, with the title "Pur-1, a zinc-finger protein that binds to purine-rich sequences, transactivates an insulin promoter in heterologous cells." The authors are G C Kennedy and W J Rutter. The protein, which they designate Pur-1 (for purine binding), binds to the GAGA boxes of the rat insulin I and II genes and the human islet amyloid polypeptide gene. Pur-1 is a potent transactivator in both pancreatic and nonpancreatic cells and is able to activate an intact insulin promoter in HeLa cells, where it is normally inactive.

The minisatellite in the diabetes susceptibility locus IDDM2 regulates insulin transcription

Giulia C. Kennedy is listed as an inventor on a patent (WO2001096523A2) related to polynucleotides related to colon cancer, along with co-inventors Sanmao Kang, Christoph Reinhard, and Anne Bennet Jefferson. A patent filed by Chiron Corporation with inventor Giulia C. Kennedy relates to DNA coding sequences of polynucleotides that are up- or down-regulated in cancer and dysplasia.

Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, and Mei R. "Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array," Genome Research 14: 414-425 (2004)

The paper presents a high-throughput genotyping platform using a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array, which uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset, enabling allele-specific hybridization to the array.

a high-throughput approach for assessment of DNA copy-number changes, through use of high-density synthetic oligonucleotide arrays containing 116,204 single-nucleotide polymorphisms

US7300788 is titled "Method for genotyping polymorphisms in humans" and was granted on November 27, 2007. The inventors are Hajime Matsuzaki, Rui Mei, Mei-Mei Shen, and Giulia C. Kennedy. The patent was assigned to Affymetrix Inc. The application number is US10/681,773, and the patent claims priority to U.S. Provisional Application Nos. 60/417,190 filed Oct. 8, 2002 and 60/470,475 filed May 14, 2003.

Molecular Classification of Thyroid Nodules Using High-Dimensionality Genomic Data

the potential for the Afirma Gene Expression Classifier to reduce unnecessary thyroid surgeries by more than half

Preoperative Diagnosis of Benign Thyroid Nodules with Indeterminate Cytology

19-month prospective, multicenter validation study with 49 clinical sites, 3789 patients, and 4812 fine-needle aspirates

Analytical Performance Verification of a Molecular Diagnostic for Cytology-Indeterminate Thyroid Nodules

initial public offering of 5,000,000 shares of its common stock at a price to the public of $13.00 per share

Prior to joining Veracyte, she was a Senior Director at Affymetrix, Inc., a microarray technology company, where she served from January 2000 to March 2008.

Giulia C. Kennedy, Ph.D. has served as our Chief Scientific Officer since September 2008. From April 2008 to September 2008, Dr. Kennedy served as our Senior Vice President of Research and Development. Prior to joining Veracyte, from January 2000 to March 2008, she was a Senior Director at Affymetrix, Inc. Prior to joining Veracyte, Dr. Kennedy was a Senior Director at Affymetrix, Inc., a microarray technology company, where she served from January 2000 to March 2008. Prior to joining Affymetrix, Dr. Kennedy served in scientific roles at Chiron Corporation and Millennium Pharmaceuticals, Inc., both of which were biotechnology companies. Dr. Kennedy holds a B.S. in Applied Science from Youngstown State University and a Ph.D. in Biochemistry from Case Western Reserve University School of Medicine and completed postdoctoral training in the Biochemistry Department and Hormone Research Institute at the University of California, San Francisco.

Application Number: US12/592,065 Filing Date: November 17, 2009 Publication/Grant Date: March 11, 2014 Assignee: Veracyte Inc Inventors: Giulia C. Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee, Jonathan I. Wilde

The patent has a priority date of 2009-05-07 and was granted on 2014-03-11. ... The inventors include Giulia C. Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee, and Jonathan I. Wilde.

Percepta Bronchial Genomic Classifier

The paper reports on the Percepta bronchial genomic classifier, which was developed and clinically validated to provide more accurate classification of lung nodules and lesions that are inconclusive by bronchoscopy, using bronchial brushing specimens.

The article is titled "Analytical performance of a bronchial genomic classifier" and was published in 2016 by authors including Zhanzhi Hu, Duncan Whitney, Jessica R. Anderson, Manqiu Cao, Christine Ho, Yoonha Choi, Jing Huang, Robert Frink, Kate Porta Smith, Robert Monroe, Giulia C. Kennedy, and P. Sean Walsh.

In fine needle aspiration biopsies (FNAs), genetic alterations were detected in 19 of 44 malignant samples (43% sensitivity) and 7 of 44 histopathology benign samples (84% specificity), and when tissue samples were added, 50% of histopathology malignant samples harbored a genetic alteration while 20% of benign samples were also mutated.

authored by Moraima Pagan, Richard T. Kloos, and others including Giulia C. Kennedy, published on January 11, 2016 in BMC Bioinformatics.

The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes

Envisia Genomic Classifier

We are employing the same machine learning methods that are being used in other fields such as social media and self-driving cars, but applying them to thyroid cancer diagnosis

initiated the transition to the next-generation Afirma Genomic Sequencing Classifier (GSC), which can save an estimated 70% of benign patients from unnecessary thyroid surgery

The ensemble machine learning algorithms, which underlie the performance of Afirma GSC, derive from years of thoughtful scientific research, data analysis and statistical modeling

Usual Interstitial Pneumonia Can Be Detected in Transbronchial Biopsies Using Machine Learning

These new data underscore the scientific rigor behind the Envisia Genomic Classifier and should give physicians and their patients even more confidence in the test's results.

the new scientific, clinical and medical affairs department headed by Giulia C. Kennedy, Ph.D., who has served as chief scientific officer since the company's founding in 2008

Advances in next-generation sequencing have created huge amounts of genomic data, which offer the promise of solving difficult clinical questions. The challenge for diagnostics companies lies in developing machine learning algorithms that can harness this data and realize its potential to have a real and meaningful impact on patient care.

Since the commercial introduction of Afirma in 2011, Veracyte has performed over 100,000 genomic tests, and estimates it has saved more than 40,000 patients from unnecessary thyroid surgery.

The models classified UIP on transbronchial biopsy samples with a receiver-operating characteristic area under the curve of approximately 0.9 in cross-validation. The final model showed sensitivity of 70% and specificity of 88% in the test set.

Identification of usual interstitial pneumonia pattern using RNA-Seq and machine learning: challenges and solutions

was published on May 9, 2018, with authors Yoonha Choi, Tiffany Ting Liu, Daniel G. Pankratz, Thomas V. Colby, Neil M. Barth, David A. Lynch, P. Sean Walsh, Ganesh Raghu, Giulia C. Kennedy, and Jing Huang.

Our RNA sequencing-based platform enables us to derive unprecedented amounts of rich genomic content from clinical samples.

Performance of a Genomic Sequencing Classifier for the Preoperative Diagnosis of Cytologically Indeterminate Thyroid Nodules

Giulia C. Kennedy, Ph.D., has served as our Chief Scientific Officer since September 2008 and became our Chief Medical Officer in January 2018.

As more is understood about the genomic makeup of thyroid cancer biology, physicians may be able to further refine their treatment plans for patients using ever-more-granular genomic information

Veracyte Receives Final Medicare Coverage Policy for Envisia Genomic Classifier

Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms

Yangyang Hao, Quan-Yang Duh, Richard T. Kloos, Joshua Babiarz, R. Mack Harrell, S. Thomas Traweek, Su Yeon Kim, Grazyna Fedorowicz, P. Sean Walsh, Peter M. Sadow, Jing Huang, and Giulia C. Kennedy

Use of a molecular classifier to identify usual interstitial pneumonia in conventional transbronchial lung biopsy samples: a prospective validation study

Lung nodules are often challenging to diagnose using traditional tools, which can lead to unnecessary invasive procedures or to delayed treatment

Dr. Kennedy was the first executive hire by Ms. Anderson in 2008 when Veracyte was founded.

Analytical Verification Performance of Afirma Genomic Sequencing Classifier in the Diagnosis of Cytologically Indeterminate Thyroid Nodules

The analytical sensitivity analysis showed that Afirma GSC calls are tolerant to variation in RNA input amount (5-30 ng), and up to 75% dilution of malignant FNA material, and analytical specificity studies demonstrated Afirma GSC remains accurate in presence of up to 75% blood or 30% genomic DNA.

was authored by Yangyang Hao, Yoonha Choi, Joshua E. Babiarz, Richard T. Kloos, Giulia C. Kennedy, Jing Huang, and P. Sean Walsh, and was published in Frontiers in Endocrinology on July 4, 2019.

Analytical and Clinical Validation of Expressed Variants and Fusions From the Whole Transcriptome of Thyroid FNA Samples

Filed: September 12, 2017; Date of Patent: October 15, 2019 Inventors: Jonathan I. Wilde, Darya Chudova, Giulia C. Kennedy Assignee: Veracyte Inc

The final GSC model uses 1232 genes and four clinical covariates—age, pack-years, inhaled medication use, and specimen collection timing.

Giulia C. Kennedy, Ph.D., serves as chief scientific officer and chief medical officer of Veracyte and authored a publication demonstrating the Envisia classifier's ability to identify a UIP pattern of lung fibrosis in patients with interstitial lung disease.

The real-world findings published in CHEST show that use of the Percepta classifier significantly alters physicians' pre-test clinical plans for an invasive procedure, enabling some patients to safely avoid the potential morbidity, mortality and cost associated with unnecessary, invasive procedures without delaying or shifting the stage of diagnosis among those who have lung cancer.

Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts

Authors: Yoonha Choi, Jianghan Qu, Shuyang Wu, Yangyang Hao, Jiarui Zhang, Jianchang Ning, Xinwu Yang, Lori Lofaro, Daniel G. Pankratz, Joshua Babiarz, P. Sean Walsh, Ehab Billatos, Marc E. Lenburg, Giulia C. Kennedy, Jon McAuliffe, Jing Huang

Improving lung cancer risk stratification leveraging whole transcriptome RNA sequencing and machine learning across multiple cohorts.

The study was published in The Journal of Clinical Endocrinology and Metabolism in 2021 by Hu, M. I., Waguespack, S. G., Dosiou, C., Ladenson, P. W., Livhits, M. J., Wirth, L. J., Sadow, P. M., Krane, J. F., Stack, B. C., Zafereo, M. E., Ali, S. Z., Weitzman, S. P., Hao, Y., Babiarz, J. E., Kennedy, G. C., and Kloos, R. T.

These findings give us confidence that the Percepta Genomic Atlas will be able to accurately detect gene alterations that may allow patients to be treated with targeted therapies that are available now and that will be available in the future. Importantly, we believe it will be able to provide this critical information near the time of diagnosis, enabling earlier and more appropriate treatment.

What is really exciting about these data is that doctors will be able to tell their patients with suspicious lung 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

Afirma Genomic Sequencing Classifier and Xpression Atlas Molecular Findings in Consecutive Bethesda III-VI Thyroid Nodules.

Giulia C. Kennedy, Ph.D., was named Veracyte's global chief scientific officer and chief medical officer. In this expanded role, Dr. Kennedy oversees a worldwide team of research and development, medical affairs, data science and clinical affairs professionals to fuel innovative research and the development of Veracyte's genomic and other diagnostic tests.

Both pulmonologists and patients are often confronted by a great deal of uncertainty when faced with a non-diagnostic bronchoscopy. These findings reinforce the clinical value and benefits of Veracyte's Percepta GSC, suggesting that the test could help improve outcomes for early-stage lung cancer patients by supporting recommended treatment approaches, reducing diagnostic delays and preventing unnecessary procedures.

these discussions reinforce the intended clinical value of our test, which is to enable physicians to make a confident diagnosis of IPF, without the need for invasive surgery.

Preoperative Identification of Medullary Thyroid Carcinoma (MTC): Clinical Validation of the Afirma MTC RNA-Sequencing Classifier

was published in 2022 with authors including Gregory W. Randolph, Giulia C. Kennedy, and Richard T. Kloos.

On December 9, 2022, Veracyte, Inc. and Giulia C. Kennedy, Ph.D., the Company's Global Chief Scientific Officer and Chief Medical Officer, agreed that Dr. Kennedy would depart the Company effective December 31, 2022.

Acuamark Diagnostics ... today announced the appointment of Giulia Kennedy, Ph.D., former Chief Scientific and Chief Medical Officer of Veracyte, to its board of directors. Prior to joining Veracyte, Dr. Kennedy was at Affymetrix, where she accelerated commercialization of the company's platform into multiple emerging markets. She holds a Ph.D. degree in biochemistry, and completed postdoctoral training at the University of California at San Francisco in the Biochemistry Department and Hormone Research Institute.

Ms. Kennedy departed the company December 31, 2022 after a long and successful career of leading the company as its Global Chief Scientific Officer and Chief Medical Officer whereby she was instrumental in developing the company's innovative products.

US 11,639,527, granted on May 2, 2023, assigned to Veracyte, Inc., which covers "Methods for sequencing and analysis of nucleic acids and determining that a subject is positive for a non-usual interstitial pneumonia subtype." The patent lists Giulia C. Kennedy as one of the assignors, along with Daniel Pankratz, Su Yeon Kim, Yoonha Choi, Jing Huang, and Moraima Pagan.

PinkDx, Inc. ... today announced its launch with $40 million in Series A financing ... co-founded by Bonnie Anderson, chair and CEO, and Giulia C. Kennedy, Ph.D., chief scientific officer.

Inventors: Kennedy, Giulia C.; Huang, Jing; CHOI, Yoonha; Pankratz, Daniel; Walsh, Patric Sean Assignee: Veracyte Inc Publication Date: 2024-05-07

We are delighted to have a life sciences industry veteran of Dr. Epstein's caliber join the PinkDx board. His extensive expertise in genomics, clinical research and health economics will be especially important as we develop and seek reimbursement for our first test.

US 12,110,554 B2 titled "Methods for classification of tissue samples as positive or negative for cancer" lists inventors Giulia C. Kennedy, Bonnie H. Anderson, Darya I. Chudova, Eric T. Wang, Hui Wang, Moraima Pagan, Nusrat Rabbee, and Jonathan I. Wilde, and is assigned to Veracyte, Inc.

We are excited for Dr. Francis to join the PinkDx team to advance our work in addressing unmet medical needs uniquely faced by women

PinkDx Announces Second Close of Upsized Series A Financing with New Investors Blue Venture Fund, Sandbox Clinical Ventures and BEVC

Title: Methods for treatment of thyroid cancer Inventors: Giulia C. Kennedy, San Francisco, CA (US); Darya I. Chudova, San Jose, CA (US); Eric T. Wang, Milpitas, CA (US); Jonathan I. Wilde, Burlingame, CA (US); Bonnie H. Anderson, Half Moon Bay, CA (US); Hui Wang, San Bruno, CA (US); Moraima Pagan, San Francisco, CA (US); and Nusrat Rabbee, South San Francisco, CA (US)

Women undergoing hysterectomy were enrolled in an exploratory study, PNK001, wherein vaginal swabs, ectocervical swabs, endocervical cytobrushes, and endometrial tissue were obtained. ... Classifiers trained using expressed genes and variant counts distinguished 5 benign from 15 malignant cases in cytobrush, ectocervical, and vaginal swab samples, with average receiver operating characteristic area under the curve values of 0.6 to 0.96 in cross-validation.

Giulia Kennedy, Ph.D. is the Co-Founder and Chief Scientific Officer of PinkDx, Inc., a molecular diagnostic company focused on women's gynecological cancers. Prior to co-founding PinkDx, she was Chief Scientific Officer and Chief Medical Officer of Veracyte, Inc. and led the development and commercialization of eight genomic diagnostic tests that changed the standard of patient care.

Whole-transcriptome sequencing and machine learning detect molecular signatures of endometrial cancer in non-invasive vaginal swabs

The assumption has always been that you have to sample the uterus to understand what's happening in the uterus. Our findings challenge that assumption. We show that molecular signals associated with endometrial cancer can be detected from a vaginal swab — a result with meaningful implications for how we rethink the diagnostic experience for women. ... A molecular biologist and diagnostics innovator, she brings deep expertise in genomics, bioinformatics, and translational research. Prior to PinkDx, Kennedy was the chief scientific officer and chief medical officer of Veracyte, where she developed and validated genomic classifiers that enabled less invasive diagnostic pathways.

Giulia Kennedy, PhD, senior director of genomics collaborations at Affymetrix. Kennedy et al. publishing in Nature Biotech in 2003 and Matsuzaki et al. publishing in Genome Research and Nature Methods in 2004.

a women's healthcare company she founded in 2022

The research involved testing a molecular classifier called the Envisia Genomic Classifier (Veracyte; San Francisco), which had a high positive predictive value for identifying usual interstitial pneumonia, and could be used in place of surgical lung biopsy to confirm a diagnosis of idiopathic pulmonary fibrosis (IPF).

Kennedy et al. (1995) showed that the ILPR is capable of transducing a transcriptional signal in pancreatic beta cells, with a long ILPR possessing greater activity than a short ILPR. Kennedy, G.C., German, M.S. & Rutter, W.J. published "The minisatellite in the diabetes susceptibility locus IDDM2 regulates insulin transcription" in Nature Genetics 9, 293-298 (1995).

Affymetrix was awarded US Patent No. 8,679,758 for "Complexity management of genomic DNA," with Giulia Kennedy named as one of the inventors along with Hajime Matsuzaki, Xing Su, Sean Walsh, and Rui Mei.

The paper presents a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays, with call rates>99%, reproducibility>99.97%, and accuracy (as measured by inheritance in trios and concordance with the HapMap Project) >99.7%.

Giulia Kennedy was a scientist at Millennium Pharmaceuticals, where she implemented genomic and genetic approaches to uncover diabetes susceptibility genes. Before Millennium, she was a scientific leader for the colon cancer and breast cancer gene discovery efforts at Chiron Corporation, resulting in the identification of oncology markers for therapeutic drug development. Dr. Kennedy has published more than 50 articles in peer-reviewed scientific journals and is a co-inventor on more than 20 patents.

Slater et al. (2005) introduced a high-resolution method for the detection of chromosomal abnormalities using high-density synthetic oligonucleotide Affymetrix arrays containing 116,206 SNPs in the American Journal of Human Genetics.

The research involved prospectively obtained FNABs from 716 nodules with more than 3,000 features measured using microarrays, with BRAF V600E labels established for training (n=181) and independent test (n=535) sets using a sensitive quantitative PCR assay. The results showed high positive (90.4%) and negative (99.0%) percent agreement with qPCR on the test set.

Machine learning from concept to clinic: Reliable detection of BRAF V600E DNA mutations in thyroid nodules using high-dimensional RNA expression data

Patent 12297503 is a Veracyte invention relating to compositions, kits, and methods for molecular profiling and cancer diagnostics, including genomic DNA markers associated with cancer. In particular, it provides molecular profiles associated with thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.

One of her patents (6664054) was assigned to Chiron Corporation and filed in January 2001, relating to DNA coding sequences of polynucleotides that are up- or down-regulated in cancer and dysplasia.

The Affymetrix patent on "Methods and kits for genotyping ultra-high-complexity DNA" (Publication number 20040185475) lists Giulia Kennedy and Manqiu Cao as the inventors. The patent application was filed on December 17, 2003 and published on September 23, 2004.

Guilia C. Kennedy filed a patent at Chiron Corporation on January 31, 2001 related to DNA coding sequences of polynucleotides that are up- or down-regulated in cancer and dysplasia.

Kennedy et al. (1995) showed that the ILPR (insulin-linked polymorphic region/minisatellite) is capable of transducing a transcriptional signal in pancreatic beta cells, with a long ILPR possessing greater activity than a short ILPR.

Machine learning classifiers trained on tissue samples achieved receiver operating characteristic area under the curve (AUC) values of 0.97 and 0.98 on an independent test set.

Kennedy, G. with German, M., Rutter, W.J., and others published "The insulin gene promoter: A simplified nomenclature" in Diabetes, Volume 44, Issue 8, pages 1002-1004, published in 1995. The authors include M. German, S. Ashcroft, K. Docherty, H. Edlund, T. Edlund, S. Goodison, H. Imura, G. Kennedy, O. Madsen, D. Melloul, L. Moss, K. Olson, M. A. Permutt, J. Philippe, R. P. Robertson, W. J. Rutter, P. Serup, R. Stein, and D. Steiner. This was a peer-reviewed letter to the journal that has received 150 citations according to Scopus.

Kennedy et al, Nature Biotech, 2003

The study objective was to develop a molecular test that distinguishes benign and malignant thyroid nodules using fine-needle aspirates (FNA), using mRNA expression analysis to measure more than 247,186 transcripts in 315 thyroid nodules.

Giulia Kennedy, Veracyte's chief scientific officer, told PGx Reporter that the company's goal was to make this validation as "real-world an experience as possible." ... Additionally, she said the study was the "largest conducted in the US for the diagnosis of thyroid nodules."

first commercial product, which was launched in January 2011, is the Afirma Thyroid FNA Analysis. It combines cytopathology with the firm's Afirma Gene Expression Classifier gene expression test, which includes a 142-gene signature, for assessing thyroid nodule fine needle aspirate biopsies that are neither clearly benign nor malignant based on cytology review. ... Veracyte was founded in 2006 as Calderome, but changed its name to Veracyte in early 2008.

Veracyte, Inc. Announces Closing of Initial Public Offering

"Classification of usual interstitial pneumonia in patients with interstitial lung disease: assessment of a machine learning approach using high-dimensional transcriptional data" by Kim SY, Diggans J, Pankratz D, Huang J, and colleagues including Kennedy GC, published in Lancet Respir Med in June 2015; 3(6):473-82.

Giulia C. Kennedy, Ph.D., chief scientific officer of Veracyte, presented data demonstrating the clinical validity of the Envisia classifier during a private event at the conference.

Pankratz DG, Choi Y, Imtiaz U, Fedorowicz GM, Anderson JD, Colby TV, Myers JL, Lynch DA, Brown KK, Flaherty KR, Steele MP, Groshong SD, Raghu G, Barth NM, Walsh PS, Huang J, Kennedy GC, and Martinez FJ

Since its Afirma solution became available in 2011, the company has touched over 325,000 patients with Afirma and helped more than 40,000 patients avoid having all or part of their thyroids removed unnecessarily.

identifies at least one third more benign thyroid nodules among those deemed indeterminate by cytopathology, as compared to the original Afirma test

The genomic sequencing classifier had a sensitivity of 91% (95% CI, 79-98)

was published by Patel KN and colleagues, including Kennedy GC, in JAMA Surgery in September 2018 (volume 153, issue 9, pages 817-824).

Kloos RT, Traweek ST, Kennedy GC, and Lanman (along with other co-authors) authored a study on "Performance of a Genomic Sequencing Classifier for the Preoperative Diagnosis of Cytologically Indeterminate Thyroid Nodules." This was published in JAMA Surgery in 2018, specifically September 1, 2018, Volume 153(9):817-824.

Identification of hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms

The Afirma Xpression Atlas is enabling us to shed new light on the scope and scale of gene alterations found in medullary thyroid cancer.

said Giulia C. Kennedy, Ph.D., chief scientific officer and chief medical officer of Veracyte and an author of the new publication.

Pankratz DG, Choi Y, Huang J, Walsh PS, Neville H, Lofaro LR, Barth NM, Kennedy GC, Brown KK, and Martinez FJ

Of 48,952 Bethesda III/IV FNAs studied, 66% were benign by Afirma GSC

was published in the American Journal of Respiratory and Critical Care Medicine in 2021 (volume 203, issue 2, pages 211-220), with authors including Richeldi L, Scholand MB, Lynch DA, and Kennedy GC among others.

In the 96 patients studied, the Envisia Classifier achieved a specificity of 92.1% and a sensitivity of 60.3% for histology-proven UIP pattern, while local radiologists identified UIP with a sensitivity of 34.0% and specificity of 96.9%.

The classifier had 100% sensitivity (21/21 MTC FNAB specimens correctly called positive; 95% confidence interval = 83.9-100%) and 100% specificity (190/190 non-MTC FNAs correctly called negative; CI = 98.1-100%). The article was published in Thyroid, 2022 Sep;32(9):1069-1076 with DOI: 10.1089/thy.2022.0189.

Acuamark Diagnostics has appointed Giulia Kennedy, Ph.D., formerly global chief scientific officer and chief medical officer of diagnostics company Veracyte, to its board of directors.

The meta-analysis examined 13 independent real-world post-validation studies and found that the GSC demonstrated sensitivity, observed specificity, observed positive predictive value, and negative predictive value of 97%, 88%, 65%, and 99% respectively.

In the primary validation set, sensitivity and specificity for low-risk classification were 96% and 42%, whereas sensitivity and specificity for high-risk classification was 58% and 90%, respectively.

was authored by Lamb CR, Rieger-Christ KM, Reddy C, Huang J, Ding J, Johnson M, Walsh PS, Bulman WA, Lofaro LR, Wahidi MM, Feller-Kopman DJ, Spira A, Kennedy GC, and Mazzone PJ, and was published in Chest in April 2024 (165(4):1009-1019).

Nearly 2-year-old PinkDx is led by serial life sciences entrepreneur Bonnie Anderson.

The financing was co-led by Catalio Capital Management, LP, and The Production Board. Other investors include Mountain Group Partners, Byers Capital and Mayo Clinic. ... Kennedy previously served as chief scientific officer and chief medical officer of Veracyte.

Early-Stage Firm PinkDx Closes $45M Upsized Series A Financing Round

She holds a Ph.D. degree in biochemistry, and completed postdoctoral training at the University of California at San Francisco in the Biochemistry Department and Hormone Research Institute.

PinkDx says early results for accuracy have been very positive, and it has now started clinical validation trials in 12 major medical centers including Mayo Clinic and Columbia University. If the studies go as planned, the swabs may be available across the U.S. as soon as mid-2027.

The exploratory study, titled PNK001 (NCT6460818), enrolled 236 participants between February and November 2024. ... generated sequencing data from swab, cytobrush, and tissue samples representing 27 PNK001 participants and 46 Cooperative Human Tissue Network samples

The PNKO02 study, known as the PROACTION (Prospective Accrual to Investigate Reproductive Cancers in Women) study, is now underway and is being conducted at 16 sites purposefully chosen to build diversity into the trial. ... The vaginal swab will come to market as a laboratory developed test. The company expects to validate its first product by the end of this year and launch by mid-2027.

The paper by Matsuzaki et al., titled "Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays," was published in Nature Methods 1:109-111 (2004).

Kennedy has served as Director/Board Member at Astarte Medical Partners, Inc. since July 16, 2019. Astarte Medical Partners is described as a company that develops clinical intelligence software to improve outcomes for children with medical complexity.

Kennedy holds a doctorate degree from Case Western Reserve University and The University of California, San Francisco, and an undergraduate degree from Youngstown State University.

Giulia Kennedy is listed as a co-author on a meta-analysis study examining real-world performance of the Afirma Genomic Sequencing Classifier (GSC). This 2022 publication in The Journal of Clinical Endocrinology and Metabolism compared real-world performance to the 2018 validation study, which reported sensitivity of 91%, specificity of 68%, positive predictive value of 47%, and negative predictive value of 96%.

This paper describes the Dynamic Model-based (DM) algorithm, which is the default algorithm applied by Affymetrix, Inc. to decide genotype calls.

Liu et al., "Algorithms for large-scale genotyping microarrays," was published in Bioinformatics, volume 19(18), pages 2397-2403 (2003). The authors include Wei-Min Liu, Xiaojun Di, Geoffrey Yang, Hajime Matsuzaki, Jing Huang, Rui Mei, Thomas B. Ryder, Teresa A. Webster, Shoulian Dong, Guoying Liu, Keith W. Jones, Giulia C. Kennedy, and David Kulp.

The paper addresses genetic studies aimed at understanding the molecular basis of complex human phenotypes through genotyping of many thousands of single-nucleotide polymorphisms (SNPs) across large numbers of individuals.

"Large-scale genotyping of complex DNA" by Kennedy GC, Matsuzaki H, Dong S and colleagues, published in Nature Biotechnology in 2003 (volume 21, pages 1233-1237).

"Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays" by Xiaojun Di, Hajime Matsuzaki, Teresa A. Webster, Earl Hubbell, Guoying Liu, Shoulian Dong, Dan Bartell, Jing Huang, Richard Chiles, Geoffrey Yang, Mei-mei Shen, David Kulp, Giulia C. Kennedy, Rui Mei, Keith W. Jones, and Simon Cawley, published in Bioinformatics 21(9): 1958-1963 (2005).