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Seth Brodie at a microscope beside a live-cell imaging system, National Cancer Institute

Seth A. Brodie, Ph.D.

Single-Cell Genomics Consultant

Molecular biologist with twenty years in oncology, genomics and epigenetics — spanning academic research, the National Cancer Institute, and instrumentation R&D. Deep hands-on experience across single-cell platforms, assay development and difficult sample preparation.

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Experience

Levitas Bio

April 2021 – August 2026

Associate Director, Research and Development — Biology

  • Project lead on development of applications and products complementing a portfolio of tools using magnetic levitation for cellular sample preparation.
  • Developed nuclei extraction and purification methods for single-cell and single-nuclei genomics.
  • Led cellular phenotype assays and screens, and drug discovery assay development.
  • Application development on a high-throughput screening automation platform.
  • Customer-facing: field demonstrations, installation and team training.

Factorial Bio

2024

Consultant

  • Advised the CEO and CTO on single-cell sequencing applications and methods.

National Cancer Institute / Leidos Biomedical Research

2015 – April 2021

Senior Scientist — Functional Genomics, Cancer Genome Research Lab

  • Team manager and lead scientist on projects discovering and validating the biological function of rare genomic variants in cancers and hematological syndromes.
  • NAT10/ThumpD1 variants affecting tRNA biology in bone marrow failure syndromes; IKZF1 variants affecting hematopoiesis; variant-driven alternative splicing.
  • snCNVseq and snRNAseq to characterize tumor heterogeneity and metastatic evolution.
  • Member of a molecular tumor board — assessed variants of unknown significance for patient inclusion in a clinical trial of Olaparib (NCT03375307).
  • Primary consultant to Principal Investigators on functional genomics studies.
  • Managed a team of research associates and post-baccalaureate scientists, and a $100K annual budget.

Scientific training

Emory University, Winship Cancer Institute — Hematology & Oncology

2010 – 2015

Postdoctoral Fellow, laboratory of Dr. Johann Brandes

Epigenetic reprogramming in lung cancer

Emory University — Cardiology & Biomedical Engineering

2007 – 2009

Postdoctoral Fellow, NIH-NRSA Fellow, laboratory of Dr. Hanjoong Jo

BMPRII signaling in atherosclerosis

University at Buffalo — Biochemistry & Center of Excellence in Bioinformatics

2005 – 2007

Postdoctoral Research Associate, laboratory of Dr. Marc Halfon

Pox-Meso in somatic muscle development

Education

University at Buffalo

2005

Ph.D., Biochemistry

Structure-function studies of the Tfg2 subunit of S. cerevisiae transcription factor TFIIF. Laboratory of Dr. Alfred Ponticelli.

Lehigh University

1999

B.S., Molecular Biology (minor, Anthropology)

HHMI Undergraduate Research Fellowship, 1998–1999.

Technical expertise

Single-cell & sequencing
10x Genomics, Illumina PIPseq, Scale, Parse, MissionBio Tapestri, Fluidigm C1; Illumina and Ion Torrent NGS — Ampliseq, RNAseq, ChIPseq, RIPseq
Sample preparation
Magnetic-levitation tissue, cell and nuclei preparation; FFPE tumor analysis — IHC, H&E, nucleic acid and single-nuclei extraction, spatial
Cell biology
2D and 3D human primary culture (PBMC, epithelial, endothelial), cancer and immortalized lines, hypoxia, transfection, viral production and transduction, CRISPR, siRNA/shRNA
Assays & analysis
Assay and method development, ACEA real-time cellular analysis, proximity ligation, drug sensitivity and resistance; flow cytometry and sorting; confocal, fluorescent and live-cell imaging; qPCR
Epigenetics
DNA methylation and histone modification
Computational
CellRanger, Seurat, Seven Bridges Genomics, Galaxy, Ingenuity, GeneGO, JMP; protein homology modeling and docking
Other
Surface plasmon resonance (SPR); xenograft models and husbandry; protein expression, purification and analysis

Patents

  • Particle Separator System, Materials, and Methods of Use

    U.S. Patent Application No. 18/604,367

Invited presentations

  • Magnetic Levitation Enables Preclinical Target and Translational Discoveries

    St. Jude Children's Research Hospital, Memphis, TN · September 2025

  • Levitation enables the use of challenging samples

    UCSF Diller Family Comprehensive Cancer Center, San Francisco, CA · September 2024

  • Using Magnetic Levitation as a Label-Free Sample Preparation Method for Functional and Single Cell Genomics Applications

    Egypt-Japan University of Science and Technology, Alexandria (webinar) · November 2021

Publications

23 peer-reviewed papers, 9 as first or co-first author.

  1. Xia B, Biswas K, Foo TK, et al. (incl. Brodie SA) Rare germline variants in PALB2 and BRCA2 in familial and sporadic chordoma. Human Mutation, 2022.
  2. Colli LM, Jessop L, Myers TA, et al. (incl. Brodie SA) Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus. American Journal of Human Genetics, 2021.
  3. Brodie SA, Khincha PP, Giri N, et al. Pathogenic germline IKZF1 variant alters hematopoietic gene expression profiles. Cold Spring Harbor Molecular Case Studies, 2021.
  4. Kim J, Gianferante M, Karyadi DM, et al. (incl. Brodie SA) Frequency of pathogenic germline variants in cancer-susceptibility genes in the Childhood Cancer Survivor Study. JNCI Cancer Spectrum, 2021.
  5. Fadl BR, Brodie SA, Malasky M, et al. An optimized protocol for retina single-cell RNA sequencing. Molecular Vision, 2020.
  6. Zhu B, Poeta ML, Costantini M, et al. (incl. Brodie S) The genomic and epigenomic evolutionary history of papillary renal cell carcinomas. Nature Communications, 2020.
  7. Brodie SA, Rodriguez-Aulet JP, Giri N, et al. 1q21.1 deletion and a rare functional polymorphism in siblings with thrombocytopenia-absent radius-like phenotypes. Cold Spring Harbor Molecular Case Studies, 2019.
  8. Kim J, Luo W, Wang M, et al. (incl. Brodie SA) Prevalence of pathogenic/likely pathogenic variants in the 24 cancer genes of the ACMG Secondary Findings v2.0 list in a large cancer cohort and ethnicity-matched controls. Genome Medicine, 2018.
  9. Mirabello L, Khincha PP, Ellis SR, et al. (incl. Brodie S) Novel and known ribosomal causes of Diamond-Blackfan anaemia identified through comprehensive genomic characterisation. Journal of Medical Genetics, 2017.
  10. Nickerson ML, Das S, Im KM, et al. (incl. Brodie SA) TET2 binds the androgen receptor and loss is associated with prostate cancer. Oncogene, 2017.
  11. Shi J, Hua X, Zhu B, et al. (incl. Brodie SA) Somatic genomics and clinical features of lung adenocarcinoma: a retrospective study. PLoS Medicine, 2016.
  12. Brodie SA, Li G, Harvey D, Khuri FR, Vertino PM, Brandes JC Small molecule inhibition of the CHFR-PARP1 interaction as novel approach to overcome intrinsic taxane resistance in cancer. Oncotarget, 2015.
  13. Brodie SA, Li G, Brandes JC Molecular characteristics of non-small cell lung cancer with reduced CHFR expression in The Cancer Genome Atlas (TCGA) project. Respiratory Medicine, 2015.
  14. Brodie SA, Lombardo C, Li G, et al. Aberrant promoter methylation of caveolin-1 is associated with favorable response to taxane-platinum combination chemotherapy in advanced NSCLC. PLOS ONE, 2014.
  15. Brodie SA, Li G, El-Kommos A, et al. Class I HDACs are mediators of smoke-carcinogen induced stabilization of DNMT1 and serve as promising targets for chemoprevention of lung cancer. Cancer Prevention Research, 2014.
  16. Brodie SA, Brandes JC Could valproic acid be an effective anticancer agent? The evidence so far. Expert Review of Anticancer Therapy, 2014.
  17. Kang H, Gillespie TW, Goodman M, et al. (incl. Brodie SA) Long-term use of valproic acid in United States veterans is associated with reduced risk of smoking-related head and neck cancers. Cancer, 2014.
  18. Kim CW, Song H, Kumar S, et al. (incl. Brodie S) Anti-inflammatory and anti-atherogenic role of BMP receptor II in endothelial cells. Arteriosclerosis, Thrombosis, and Vascular Biology, 2013.
  19. Pillai RN*, Brodie SA*, Sica GL, et al. CHFR protein expression predicts outcomes to taxane-based first line therapy in metastatic NSCLC. Clinical Cancer Research, 2013.
  20. Tiwari D, Brodie SA, Brandes JC Targeted therapy of NSCLC. Therapeutic Advances in Respiratory Disease, 2012.
  21. Ghazy MA*, Brodie SA*, Ammerman ML, Ziegler LM, Ponticelli AS Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II. Molecular and Cellular Biology, 2004.
  22. Faitar SL, Brodie SA, Ponticelli AS Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites. Molecular and Cellular Biology, 2001.
  23. Vander Zwan C, Brodie SA, Campanella JJ The intraspecific phylogenetics of Arabidopsis thaliana in worldwide populations. Systematic Botany, 2000.

Editorial & review service

  • Clinical Trial Genetics Review Panel, 2017–2021 — Phase II study of Olaparib in metastatic/advanced urothelial carcinoma with DNA-repair defects (NCI/AstraZeneca)
  • Ad hoc reviewer — Cancer Research (2018–2020), Brazilian Journal of Medical and Biological Research (2018–2020), PLOS Genetics (2017), Cancer (2014), Journal of Clinical Oncology (2014)

Teaching & mentoring

Gwinnett School of Mathematics, Science and Technology

2009 – 2010

Teacher, Science Department — developed curriculum for two new advanced biology courses

Emory University, Department of Biology

2008 – 2009

Lecturer, Foundations of Modern Biology Laboratory I & II

University at Buffalo, Department of Biochemistry

2001 – 2007

Lecturer, graduate-level biochemistry; instructor, MED STEP program; teaching assistant

Professional memberships

AACR (2011–2022) · IASLC (2012–2022) · ASHG (2020–2022)