High-density oligonucleotide arrays for genotyping single-nucleotide polymorphisms genome-wide. The 10K array genotyped over 10,000 SNPs per individual on a single array (Genome Research, 2004) and the 100K set scored 116,204 SNPs on a pair of arrays with call rates above 99% (Nature Methods, 2004). A 2006 NHGRI primer cites "Kennedy et al, Nature Biotech, 2003" as the reference for the GeneChip Mapping Assay, and Kennedy is a co-inventor on Affymetrix's US 7,300,788, "Method for genotyping polymorphisms in humans".

The sample-preparation method behind the GeneChip Mapping arrays: restriction digestion fractionates the genome, a specific fractionated subset is amplified with a single primer, and alleles are read by allele-specific hybridization to the array. Described in "Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array" (Genome Research, 2004), on which Kennedy is a co-author, and introduced in "Large-scale genotyping of complex DNA" (Nature Biotechnology, 2003), on which she is first author.

Veracyte's first commercial product, launched in January 2011 as the Afirma Thyroid FNA Analysis. It combines cytopathology with a gene expression test, described in trade press as a 142-gene signature, to identify benign nodules among thyroid fine-needle aspirates that cytology leaves indeterminate. Developed from 315 nodules and more than 247,186 transcripts (JCEM, 2010) and validated prospectively at 49 sites in 3,789 patients (NEJM, 2012), with Kennedy as last and second author respectively.

The second-generation Afirma test, built on whole-transcriptome RNA sequencing and ensemble machine learning algorithms. Veracyte announced pivotal validation data on May 4, 2017 and began transitioning patients to the GSC that quarter, saying it could save an estimated 70% of patients with benign nodules from unnecessary surgery. The JAMA Surgery validation (2018) found it identifies at least one third more benign nodules than the original test with 91% sensitivity. The companion Afirma Xpression Atlas, launched May 2018, reports gene variants and fusions from the same sample.

The sequencing platform that replaced microarrays in Veracyte's second-generation tests. Kennedy described it at the 2018 Xpression Atlas launch: "Our RNA sequencing-based platform enables us to derive unprecedented amounts of rich genomic content from clinical samples." The Afirma GSC, Percepta GSC and Envisia classifiers are built on it, and PinkDx applies whole-transcriptome sequencing to vaginal swab samples in its endometrial cancer programme.

The algorithmic approach behind Veracyte's sequencing-era classifiers and PinkDx's swab test. Kennedy said in 2017 that "the ensemble machine learning algorithms, which underlie the performance of Afirma GSC, derive from years of thoughtful scientific research, data analysis and statistical modeling", and that the company was "employing the same machine learning methods that are being used in other fields such as social media and self-driving cars". The 2019 BMC Systems Biology paper, with Kennedy as last author, describes a trio of machine learning algorithms for Hürthle cell nodules.

The algorithmic approach behind Veracyte's sequencing-era classifiers and PinkDx's swab test. Kennedy said in 2017 that "the ensemble machine learning algorithms, which underlie the performance of Afirma GSC, derive from years of thoughtful scientific research, data analysis and statistical modeling", and that the company was "employing the same machine learning methods that are being used in other fields such as social media and self-driving cars". The 2019 BMC Systems Biology paper, with Kennedy as last author, describes a trio of machine learning algorithms for Hürthle cell nodules.

The sequencing platform that replaced microarrays in Veracyte's second-generation tests. Kennedy described it at the 2018 Xpression Atlas launch: "Our RNA sequencing-based platform enables us to derive unprecedented amounts of rich genomic content from clinical samples." The Afirma GSC, Percepta GSC and Envisia classifiers are built on it, and PinkDx applies whole-transcriptome sequencing to vaginal swab samples in its endometrial cancer programme.

Veracyte's lung cancer diagnostic, launched April 16, 2015, which classifies lung nodules and lesions that are inconclusive by bronchoscopy using bronchial brushing specimens. The next-generation Percepta Genomic Sequencing Classifier became available to physicians on June 26, 2019, and 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.

Veracyte's classifier for idiopathic pulmonary fibrosis, launched at the CHEST Annual Meeting on October 25, 2016, where Kennedy presented clinical validity data. It identifies the usual interstitial pneumonia pattern in conventional transbronchial lung biopsy samples, offering an alternative to surgical lung biopsy; the prospective validation appeared in The Lancet Respiratory Medicine in 2019 and a study of the classifier as a complement to high-resolution CT in AJRCCM in 2021. Medicare coverage through the Palmetto GBA MolDX program took effect April 1, 2019.

The sequencing platform that replaced microarrays in Veracyte's second-generation tests. Kennedy described it at the 2018 Xpression Atlas launch: "Our RNA sequencing-based platform enables us to derive unprecedented amounts of rich genomic content from clinical samples." The Afirma GSC, Percepta GSC and Envisia classifiers are built on it, and PinkDx applies whole-transcriptome sequencing to vaginal swab samples in its endometrial cancer programme.

The algorithmic approach behind Veracyte's sequencing-era classifiers and PinkDx's swab test. Kennedy said in 2017 that "the ensemble machine learning algorithms, which underlie the performance of Afirma GSC, derive from years of thoughtful scientific research, data analysis and statistical modeling", and that the company was "employing the same machine learning methods that are being used in other fields such as social media and self-driving cars". The 2019 BMC Systems Biology paper, with Kennedy as last author, describes a trio of machine learning algorithms for Hürthle cell nodules.

PinkDx's first product in development: a clinician-collected vaginal swab, with no speculum required, for endometrial cancer in women with abnormal bleeding. The sample is shipped to the PinkDx laboratory in California and an algorithm classifies it as positive or not positive for endometrial cancer. The exploratory PNK001 study (NCT06460818) showed that molecular signals of endometrial cancer can be read from a vaginal swab by whole-transcriptome sequencing and machine learning (IJGC, 2026), and the PROACTION study (NCT06527157) is validating the test.

The sequencing platform that replaced microarrays in Veracyte's second-generation tests. Kennedy described it at the 2018 Xpression Atlas launch: "Our RNA sequencing-based platform enables us to derive unprecedented amounts of rich genomic content from clinical samples." The Afirma GSC, Percepta GSC and Envisia classifiers are built on it, and PinkDx applies whole-transcriptome sequencing to vaginal swab samples in its endometrial cancer programme.

The algorithmic approach behind Veracyte's sequencing-era classifiers and PinkDx's swab test. Kennedy said in 2017 that "the ensemble machine learning algorithms, which underlie the performance of Afirma GSC, derive from years of thoughtful scientific research, data analysis and statistical modeling", and that the company was "employing the same machine learning methods that are being used in other fields such as social media and self-driving cars". The 2019 BMC Systems Biology paper, with Kennedy as last author, describes a trio of machine learning algorithms for Hürthle cell nodules.