Development of a liquid biopsy platform that profiles circulating chromatin and the DNA methylome from 1 mL of plasma. The Precede platform interrogates a genome-wide, feature-rich space of gene promoters, gene enhancers, and methylated cfDNA giving resolution into the dynamic activation of individual genes and pathways.

Seed stage product development for founding of Precede Biosciences Inc. Tech transfer, protocol evaluation, assay development, and workflow throughput scaling, analytical and clinical POC data generation.

I built and led a Product Development team tasked to commercialize the multi-cancer early detection (MCED) assay CancerSEEK, a blood-based liquid biopsy diagnostic test designed for the detection of multiple types of cancer at earlier stages and planned to be utilized as part of routine medical care. The assay was based on circulating cell-free DNA somatic variants (SNVs, indels), aneuploidy, methylation and quantification of a defined panel of circulating proteins. CancerSEEK was developed at Johns Hopkins University (Papadopoulos, Kinzler, Vogelstein) and Thrive Earlier Detection was founded to commercialize the test. In 2019 I was on the founding team of Thrive Earlier Detection and the company was acquired by Exact Sciences in January 2021 for $2.15B.

Seed stage accelerator for the founding of Thrive Earlier Detection.

I joined FMI for the feasibility, development, analytical validation, and commercialization of blood-based clinical circulating tumor DNA assays for non-invasive cancer molecular profiling. My main focus was on Foundation Medicine's liquid biopsy product portfolio. FoundationACT was validated for use as a clinical trial assay in 2015, successfully launched as a commercial product in 2016, version 2 was launched as FoundationOne Liquid in 2018, and FoundationOne Liquid CDx received FDA approval in 2020. Foundation Medicine was fully acquired by Roche in 2018 ($2.4B outstanding shares, total company value $5.4B).Clark TA, et al. 2018. Analytical validation of a hybrid capture-based next-generation sequencing clinical assay for genomic profiling of cell-free circulating tumor DNA. J Mol Diagn. pii: S1525-1578(17)30527-5.Woodhouse R, et al. 2020. Clinical and analytical validation of FoundationOne Liquid CDx, a novel 324-Gene cfDNA-based comprehensive genomic profiling assay for cancers of solid tumor origin. PLoS One. 15(9):e0237802.I also developed patient (or clinical trial) personalized MRD assays for longitudinal analysis of plasma ctDNA as an early predictor of response and long-term outcomes. Collaborative work with Genentech indicated the assay could be used as an early surrogate trial endpoint.Wongchenko, MJ et al. On-treatment changes in circulating tumor DNA (ctDNA) level as an early predictor of clinical outcome in the LOTUS randomized phase 2 trial of 1st-line ipatasertib (IPAT) + paclitaxel (PAC) for metastatic triple-negative breast cancer (mTNBC). AACR 2018 Session MS.CL10.02 - Use of Liquid Biopsies in Clinical Trials

I was responsible for the development and operation of genomics technologies (with primary focus on next-generation DNA sequencing) at the founding of VANTAGE, a genomics facility built to serve Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center, and Vanderbilt University. I also worked within the Precision Cancer Medicine Initiative (PCMI) at Vanderbilt-Ingram Cancer Center on genomic assays for therapy selection and biomarker discovery.

Ground level research and development of a next-generation DNA sequencing method using semiconductor arrays to monitor changes in hydrogen ion concentration (H+, pH) during DNA polymerization reactions. I was part of the small founding team that achieved proof-of- principle and moved towards a commercial product with Ion Torrent's semiconductor DNA sequencing system. Ion Torrent was acquired by Life Technologies in 2010 for $375M.Rothberg JM, et al. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 475(7356):348-52. PMID: 21776081

I developed applications for isothermal and PCR-based nucleic acid amplification and detection using a high-throughput pico-droplet-based microfluidic platform. I worked with on diverse applications utilizing creative enzymology coupled with various microfluidic chip designs on a "breadboard" pre-commercial system. My focus was on the development of emPCR based selective genomic sequence enrichment assay (targeted cancer gene panels, Myriad myRisk) for next-generation sequencing. Company moved from Guilford CT to Lexington MA and I opted to stay in CT with a small team and join the founding of Ion Torrent Systems.

Developed molecular and analysis methods for gene expression studies in Neurospora crassa, a model system of genetics. My specific experimental research was in characterizing genome-wide gene expression variation related to mechanisms of speciation and somatic genome interaction and methods for non-biased selective sequence capture of coding RNAs for microarray hybridization and early next-gen DNA sequencing (Illumina/Solexa and 454). I liked solving problems as a diverse team more than the traditional academic path and found a better fit in local JM Rothberg start-ups (RainDance Technologies and Ion Torrent).

Ph.D. program in Molecular Genetics and Genomics. Research and coursework in experimental evolution, evolutionary genomics, phylogenetics, bioinformatics, and molecular evolution. I developed a novel experimental system and used molecular tools to detect somatic mutation and recombination in multi-year experimental evolution systems. Teaching assistant in Genetics, Mycology, and Evolutionary Biology.